Nol3 is a predictor of  patient outcome

ABSTRACT

The present invention features a method for determining the prognosis for survival of a cancer patient. Methods for measuring the level of NOL3 expression in a cancer cell-containing sample from a patient, and comparing the level of NOL3 expression in the sample to a reference level of NOL3 expression are also included. A higher level of NOL3 relative to the reference level correlates with decreased survival of the patient, and an equivalent or lower level of NOL3 relative to the reference level correlates with increased survival of the patient.

RELATED APPLICATIONS

This application claims priority to U.S. Provisional Application No. 61/143,517, filed Jan. 9, 2009. The entire contents of this patent application is hereby incorporated herein by reference.

BACKGROUND OF THE INVENTION

The treatment of malignant gliomas remains one of the greatest challenges facing adult and pediatric oncologists today. At the most severe end of the spectrum is glioblastoma muitiforme (GBM)—among the most malignant of cancers, with a median survival of less than 12 months and an inherent resistance to both chemo- and radio-therapeutics (DeAngelis, N. Engl. J. Med. 344, 114-123, 2001). While initial treatment of GBM with surgery, radiotherapy and chemotherapy often produces some palliation of symptoms, these tumors almost universally recur with an unrelenting progression to death. Despite great advances in our understanding of the molecular causes of GBM (Kitange et al., Curr. Opin. Oncol. 15, 187-203, 2003), there has been very little improvement in outcomes for patients with GBM.

SUMMARY OF THE INVENTION

Strategies for the treatment of malignant gliomas are urgently needed. The present invention is based, at least in part, on the discovery that NOL3 expression levels have a significant impact on clinical outcome in patients having cancer. This invention is also based on the further discovery that a reduction in NOL3 expression is necessary for synergistic inhibition of tumor cell growth affected by growth factor receptor inhibitors, e.g., tyrosine kinase inhibitors, and inhibitors of inhibitor of apoptosis proteins (IAPs). In addition, reduction of NOL3 expression was shown to sensitize cells to the pro-apoptotic effects of IAP inhibitors.

Based at least in part on the above observations, the invention features, in a first aspect, a method for determining the prognosis for survival of a cancer patient, which includes measuring a level of NOL3 expression in a cancer cell-containing sample from the patient, and comparing the level of NOL3 expression in the sample to a reference level of NOL3 expression, wherein a higher level of NOL3 relative to said reference level correlates with decreased survival of the patient, and an equivalent or lower level of NOL3 relative to said reference level correlates with increased survival of the patient.

In a second aspect, the invention pertains to a method for determining the prognosis for survival of a cancer patient, which includes measuring a level of NOL3 expression in a cancer cell-containing sample from the patient, measuring the level of survivin expression in a cancer cell-containing sample from said patient, and comparing the level of NOL3 expression in the sample to a reference level of NOL3 expression, and comparing the level of survivin expression in the sample to a reference level of survivin expression, wherein a higher level of NOL3 and a higher level of survivin relative to said reference levels correlates with decreased survival of the patient, and wherein an equivalent or lower level of NOL3 and an equivalent or lower level of survivin relative to said reference levels correlates with increased survival of said patient.

In another aspect, the present invention pertains to a method of diagnosing the grade or stage of a tumor in a subject, which includes measuring a level of NOL3 expression in a cancer cell-containing sample from said subject, and comparing the level of NOL3 expression in said sample to a reference level of NOL3 expression, wherein a higher level of NOL3 relative to said reference level correlates with worsening grade or stage of said tumor.

In yet another aspect, the present invention relates to a method of identifying a compound as an anti-cancer agent, which includes treating a cell line expressing NOL3 with the compound, and determining the change in the level of NOL3 expression following treatment, wherein a compound which reduces the level of NOL3 expression is identified as an anti-cancer agent.

In a further aspect, the present invention relates to a method of predicting responsiveness to an anti-cancer agent in a subject having cancer, wherein said anti-cancer agent reduces the expression or activity of NOL3. The method includes measuring the level of NOL3 expression in a cancer cell-containing sample from the subject, and comparing the level of NOL3 expression in the sample to a reference level of NOL3 expression, wherein a higher level of NOL3 expression relative to the reference level predicts responsiveness of the subject to the anti-cancer agent.

In an additional aspect, the present invention pertains to a method of predicting responsiveness to an IAP inhibitor, which includes, measuring the level of NOL3 expression in a cancer cell-containing sample from the subject, and comparing the level of NOL3 expression in the sample to a reference level of NOL3 expression, wherein an equivalent or lower level of NOL3 expression relative to the reference level predicts responsiveness of the subject to the IAP inhibitor.

In an yet another aspect, the present invention relates to a method of selecting a subject having cancer for a treatment regimen, which includes measuring the level of NOL3 expression in a cancer cell-containing sample from the subject, comparing the level of NOL3 expression in the sample to a reference level of NOL3 expression, and selecting the subject for a treatment regimen, wherein a subject having a higher level of NOL3 expression relative to the reference level is selected for a treatment regimen comprising an agent that reduces the expression or activity of NOL3.

In an additional aspect, the present invention relates to a method of selecting a subject having cancer for a treatment regimen, which includes, measuring the level of NOL3 expression in a cancer cell-containing sample from the subject, comparing the level of NOL3 expression in the sample to a reference level of NOL3 expression, and selecting the subject for a treatment regimen, wherein a subject having an equivalent or lower level of NOL3 expression relative to the reference level is selected for a treatment regimen comprising an IAP inhibitor.

The present invention further provides a method for selecting a subject having cancer for a treatment regimen, which includes measuring the level of NOL3 expression in a cancer cell-containing sample from the subject, comparing the level of NOL3 expression in the sample to a reference level of NOL3 expression, and selecting the subject for a treatment regimen, wherein a subject having a higher level of NOL3 expression relative to the reference level is selected for a treatment regimen comprising an agent that reduces the expression or activity of NOL3. Furthermore, the method of this aspect additionally includes, treating the selected subject, wherein the treatment comprises administering to the selected subject a therapeutically effective amount of a growth factor receptor inhibitor; and, optionally treating the selected subject with a therapeutically effective amount of an IAP inhibitor.

In yet another aspect, the present invention provides a method for selecting a subject having cancer for a treatment regimen, which includes, measuring the level of NOL3 expression in a cancer cell-containing sample from the subject, comparing the level of NOL3 expression in the sample to a reference level of NOL3 expression, and selecting the subject for a treatment regimen, wherein a subject having an equivalent or lower level of NOL3 expression relative to the reference level is selected for a treatment regimen comprising an IAP inhibitor. Furthermore, the method of this aspect additionally includes, treating the selected subject, wherein the treatment comprises administering to the selected subject a therapeutically effective amount of an IAP inhibitor.

In a further aspect, the present invention provides a method of identifying a subject having cancer who is likely to benefit from treatment with an IAP inhibitor, which includes, assaying the level of NOL3 expression in a cancer cell-containing sample from the subject, assaying the level of NOL3 expression in a reference sample, and correlating an equivalent or lower level of NOL3 expression in the cancer cell containing sample relative to the level of NOL3 expression in the reference sample with a subject who is likely to benefit from treatment with an IAP inhibitor.

In another aspect, the present invention provides a method of identifying a subject having cancer who is likely to have an increased prognosis for survival, which includes, assaying the level of NOL3 expression in a cancer cell-containing sample from the subject, assaying the level of survivin expression in a cancer cell-containing sample from the subject, assaying the level NOL3 expression in a reference sample, assaying the level of survivin expression in a reference sample, and correlating an equivalent or lower level of NOL3 and an equivalent or lower level of survivin relative to the reference levels with a subject who is likely to have an increased prognosis for survival.

In a one embodiment of the above aspects, NOL3 refers to NOL3 mRNA. In another embodiment of the above aspects, NOL3 refers to NOL3 polypeptide. In yet another embodiment of the above aspects, the level of survivin expression is a level of survivin mRNA expression or a level of survivin protein expression.

In another embodiment of the above aspects, the level of NOL3 mRNA expression in a sample is determined by a technique selected from the group including Northern blot, RT-PCR, Quantitative RT-PCR (QPCR), non-PCR amplification methods (e.g., strand displacement amplification (SDA), rolling-circle amplification (RCA), multiple-displacement amplification (MDA), transcription meditated amplification (TMA), and nucleic acid sequence based amplification (NASBA)), Luminex bead analysis, in situ hybridization, and gene expression microarray analysis.

In an additional embodiment of the above aspects, the level of NOL3 polypeptide expression in a sample is determined by a technique selected from the group including Western blot, immunohistochemistry, indirect immunofluorescence, direct immunofluorescence, mass spectrometry, intracellular flow cytometry, enzyme-linked immunosorbent assay (ELISA), and antibody microarray analysis.

In a further embodiment of the above aspects, the level of survivin expression in a sample is determined by a technique selected from the group including Northern blot, RT-PCR, Quantitative RT-PCR (QPCR), in situ hybridization, gene expression microarray analysis, Western blot, immunohistochemistry, indirect immunofluorescence, direct immunofluorescence, mass spectrometry, intracellular flow cytometry, enzyme-linked immunosorbent assay (ELISA), and antibody microarray analysis.

In another embodiment of the above aspects, survival is overall survival. In a preferred embodiment of the above aspects, survival is disease-free survival or progression free survival.

In another embodiment of the above aspects, the sample is a tumor tissue sample. In an additional embodiment of the above aspects, the reference level is obtained from a normal tissue sample.

In one embodiment of the above aspects, the cancer is a carcinoma. In a preferred embodiment of the above aspects, the carcinoma is selected from the group consisting of ovarian carcinoma, breast carcinoma, prostate carcinoma, colorectal carcinoma, and small cell lung carcinoma.

In another embodiment of the above aspects, the cancer is a glioma. In a preferred embodiment of the above aspects, the glioma is selected from the group consisting of an astrocytoma, an ependymoma, an oligodendroglioma, a mixed glioma, and glioblastoma multiforme.

In a further embodiment of the above aspects, the cancer is a sarcoma. In a preferred embodiment of the above aspects, the sarcoma is selected from the group consisting of osteosarcoma, chondrosarcoma, leiomyosarcoma, gastrointestinal stromal tumor (GIST), Ewing's sarcoma, Askin's tumor, malignant hemangioendothelioma, malignant schwannoma, and soft tissue sarcoma (e.g., alveolar soft part sarcoma, angiosarcoma, cystosarcoma phylloides, dermatofibrosarcoma, desmoid tumor, desmoplastic small round cell tumor, epithelioid sarcoma, extraskeletal chondrosarcoma, extraskeletal osteosarcoma, fibrosarcoma, hemangiopericytoma, hemangiosarcoma, Kaposi's sarcoma, liposarcoma, lymphangiosarcoma, lymphosarcoma, malignant fibrous histiocytoma, neurofibrosarcoma, rhabdomyosarcoma, and synovial sarcoma).

In yet another embodiment of the above aspects, the cancer is a hematologic malignancy. For example, the hematologic malignancy is selected from the group including acute leukemia, chronic leukemia, multiple myeloma, and lymphoma.

In one embodiment of the above aspects, the cancer comprises a high grade tumor. In a preferred embodiment of the above aspects, the tumor is selected from the group consisting of a grade III tumor, a grade IV tumor, and a recurrent tumor.

In another preferred embodiment of these aspects, a slight increase in NOL3 mRNA expression or NOL3 polypeptide expression correlates with a grade III tumor, a moderate increase correlates with a grade IV tumor, and a large increase correlates with a recurrent tumor.

In one embodiment of the above aspects, the compound of the invention is a small molecule. In another embodiment, the compound of the invention is a biologic agent. In an additional embodiment of the above aspects, the compound further inhibits growth factor receptor-mediated signaling.

In one embodiment of the above aspects, the anti-cancer agent of the invention is a small molecule. In another embodiment, the anti-cancer agent of the invention is a biologic agent. In an additional embodiment of the above aspects, the anti-cancer agent further inhibits growth factor receptor-mediated signaling. In an exemplary embodiment of the above aspects, the anti-cancer agent is an inhibitor of receptor tyrosine kinases. In another embodiment the anti-cancer agent is an epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor or an insulin-like growth factor-1 receptor (IGF-1R) tyrosine kinase inhibitor; for example, the EGFR tyrosine kinase inhibitor is PKI166 (Hoekstra et al., Clinical Cancer Research Vol. 11, 6908-6915, Oct. 1, 2005, incorporated herein by reference in its entirety) and the IGF-1R tyrosine kinase inhibitor is AEW541 (García-Echeverría et al., Cancer Cell. 2004 March; 5(3):231-9, incorporated herein by reference in its entirety). In a preferred embodiment of the above aspects, the anti-cancer agent is a platelet derived growth factor receptor (PDGFR) kinase inhibitor; for example, the PDGFR kinase inhibitor is imatinib.

In additional embodiment, the anti-cancer agent of the invention is identified according to the method of any one of the above aspects. In another embodiment, the present invention relates to a method of treating a cancer in a subject, comprising administering to the subject the anti-cancer agent identified according to the method of any one of the above aspects.

In one embodiment of the above aspects, the anti-cancer agent of the invention is administered in combination with an IAP (Inhibitor of Apoptosis Proteins) inhibitor.

In a preferred embodiment of the above aspects, the IAP inhibitor is LBW242. In another preferred embodiment the IAP inhibitors of the invention and methods of making them are disclosed in WO 2005/097791 and WO 2008/016893, both herein incorporated by reference in their entirety.

In another embodiment of the above aspects, a higher level of NOL3 mRNA expression relative to said reference level predicts responsiveness of the subject to the anti-cancer agent administered in combination with an IAP inhibitor.

In a further embodiment of the above aspects, a higher level of NOL3 polypeptide expression relative to said reference level additionally predicts responsiveness of the subject to the anti-cancer agent administered in combination with an IAP inhibitor.

In an additional embodiment of the above aspects, a subject having a higher level of NOL3 mRNA expression relative to said reference level is selected for a treatment regimen additionally comprising an IAP inhibitor.

In yet another embodiment of the above aspects, a subject having a higher level of NOL3 mRNA expression relative to said reference level is selected for a treatment regimen additionally comprising an IAP inhibitor.

In another embodiment of the above aspects, the growth-factor receptor inhibitor is imatinib.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1A: depicts the mechanism by which PDGFR and IAP inhibition synergistically results in cell death.

FIG. 1B: depicts a graph showing that LBW242 competes with full-length Smac for occupancy of the XIAP-BIR3 surface groove.

FIG. 1C: depicts a graph showing that LBW242 overcomes XIAP-BIR3-mediated repression of caspase-3 activity in a cell-free extract, resulting in activation of caspase-3 and cleavage of the fluorogenic substrate.

FIG. 1D: depicts an immunoblot showing levels of XIAP and caspase-9 in LN827 cells treated with the indicated concentration of LBW242 after immunoprecipitation of caspase-9.

FIG. 1E depicts densitometric analysis of overall cellular levels of XIAP and caspase-9 after treatment with the indicated concentration of LBW242 relative to vehicle control.

FIG. 1F depicts densitometric analysis of XIAP in complex with caspase-9 after treatment with the indicated concentration of LBW242 relative to vehicle control.

FIG. 1G: depicts a graph showing the concentration of LBW242 in plasma, brain and tumor of 3 SK-OV-3 tumor-bearing nude mice after 14 days of daily parenteral dosing of LBW242 (50 mg/kg).

FIG. 1H: depicts a graph showing the effect of LBW242 as a single agent on the growth of U87 cells.

FIG. 2A: depicts a graph showing the treatment of LN827 and U87 cells with LBW242 and imatinib.

FIG. 2B: depicts a graph showing the effect of treatment with LBW242 and imatinib on cell growth over time in LN827 and U87 cells.

FIG. 2C: depicts a blot showing the effect of imatinib and LBW242 on the activation state of PDGFR in LN827 cells.

FIG. 2D: depicts a graph showing the effect of LBW242 and AMN107 on cell growth in LN827 and U87 cells.

FIG. 3A: depicts an immunoblot showing the effect of treatment with imatinib and/or LBW242 on the release of cytoplasmic cytochrome c and Smac/Diablo in LN827 cells.

FIG. 3B: depicts a graph showing the effects of imatinib and LBW242 on the activation of caspase 3/7.

FIG. 3C: depicts graphs showing the effect of LBW242 in combination with or without imatinib or AMN107 on cellular apoptosis, cells positive for annexin V are to the right of the divider.

FIG. 4A: depicts two graphs showing the effect of LBW242 and AEW541 on cell growth and caspase activation.

FIG. 4B: depicts two graphs showing the effect of PKI166 and LBW242 on cell growth and caspase activation.

FIG. 4C: depicts an immunoblot showing the effects of LBW242 and imatinib on Akt phosphorylation and BAD phosphorylation, Akt activation was assessed by Ser473 phosphorylation.

FIG. 4D: depicts two graphs showing the effects of an Akt inhibitor (triciribine) and LBW242 on caspase-3/7 activation.

FIG. 4E: depicts a Western blot showing the effect of treatment of LN827 cells with imatinib and/or LBW242 for six hours on the phosphorylation of Erk1/2.

FIG. 4F: depicts a Western blot showing that treatment of LN827 cells with imatinib did not affect the expression of anti- or pro-apoptotic members of the BCL-2 family of proteins.

FIG. 5A: depicts RT-PCR analysis of NOL3 after treatment with imatinib.

FIG. 5B: depicts a Western blot of NOL3 expression after treatment with imatinib.

FIG. 5C: depicts a graph showing the comparison of NOL3 mRNA expression levels in normal brain tissue, compared with malignant glioma specimens.

FIG. 5D: depicts a graph showing a comparison of the expression levels of NOL3 mRNA in grade III, grade IV, and recurrent high-grade gliomas.

FIG. 5E: depicts a graph showing the correlation between high NOL3 expression in tumor specimens and inferior patient survival.

FIG. 5F: depicts an immunoblot showing the ectopic expression of NOL3 after transfection of an expression plasmid.

FIG. 5G: depicts a graph showing the effects of LBW242 and imatinib on apoptosis in cells expressing a plasmid carrying NOL3 or a control plasmid.

FIG. 5H: depicts a blot showing siRNA knockdown of NOL3 in LN827 cells.

FIG. 5I: depicts a graph showing the combined effect of NOL3 knockdown and treatment with LBW242 on cellular apoptosis.

FIG. 5J: depicts a graph showing the combined effect of NOL3 knockdown and treatment with Etoposide on cellular apoptosis.

FIG. 6A: depicts images showing tumor burden in mice treated with vehicle, AMN107, LBW242 or AMN107 and LBW242.

FIG. 6B: depicts a graph showing tumor burden in mice treated with vehicle, AMN107, LBW242 or AMN107 and LBW242.

FIG. 6C: depicts a graph showing the effects of LBW242 and/or imatinib in primary patient-derived glioma neurosphere cultures.

FIG. 6D: depicts images showing human glioblastoma neurospheres treated with LBW242 and/or imatinib.

FIG. 6E: depicts an immunoblot showing caspase-3 activation in tumor neurospheres treated for 72 hours with imatinib. AMN107(AMN), and/or LBW242(LBW)

FIG. 6F: depicts a graph showing the percent survival for mice implanted with primary human glioma orthografts and treated with AMN107. LBW242, or a combination of AMN107 and LBW242.

FIG. 7: depicts a graph showing the effect of NOL3 expression on patient survival in combination with the expression levels of the IAP survivin.

FIG. 8A: depicts graphs showing that NOL3 levels do not impart a significant difference in survival when high-grade gliomas are stratified by histological grade.

FIG. 8B: depicts graphs showing that survivin levels do not impart a significant difference in survival when high-grade gliomas are stratified by histological grade.

FIG. 9: depicts graphs showing that the combination of NOL3 and survivin levels results in a significant difference in survival in both Grade III and IV gliomas.

DETAILED DESCRIPTION OF THE INVENTION

The present invention provides methods for determining the prognosis for survival of a cancer patient. In addition, the present invention demonstrates that anti-apoptotic proteins may be important biomakers predictive of response to treatment with anti-cancer agents, such as receptor tyrosine kinase (RTK) inhibitors, and that targeting the apoptotic pathway, in conjunction with RTK inhibition, has the potential to further improve tumor response.

The invention is based, at least in part, on the observation that the anti-apoptotic protein NOL3 is highly expressed in malignant gliomas and correlates with poor survival. In particular, RTK inhibition activates the apoptotic cascade by decreasing the expression of NOL3, but does not result in downstream caspase activation. Small molecule blockade of the Inhibitor of Apoptosis Proteins (IAP) in combination with RTK inhibition results in caspase activation and apoptosis, and has synergistic anti-tumor efficacy in vitro and in vivo in orthotopic glioma models.

In order that the present invention may be more readily understood, certain terms are first defined. Additional terms are set forth throughout the detailed description.

The term “detectable probe” includes any molecule that specifically binds to a nucleic acid sequence or to a protein that is being selected for, and which can be labeled so that the required targets can be detected. For example, the probe may be radiolabeled or chemically tagged. In another example, specific monoclonal antibodies may be used to detect proteins, and said monoclonal antibody can be labeled so that the protein of interest can be detected.

The term “favorable outcome” is intended to refer to an affirmative outcome. For example, a favorable outcome may refer to overall survival or progression-free survival. More preferably, a favorable outcome may refer to disease-free survival.

The term “cancer” is intended to refer to cells or tissue containing cells that have become malignantly transformed so that they exhibit uncontrolled growth and invasive properties. Depending on the cell type involved, the cancerous cells may form a solid tumor (carcinoma, sarcoma) or may cause various types of hematologic malignancies.

The term “tumor grade” is intended to refer to the degree of abnormality of cancer cells. In one aspect, tumor grade is a measure of differentiation. In another aspect, tumor grade is the extent to which cancer cells are similar in appearance and function to healthy cells of the same tissue type. Tumor grade may be described by four degrees of severity (i.e., grades 1, 2, 3, and 4) based on the microscopic appearance of cancer cells. For example, the cells of Grade 1 tumors are often well-differentiated or low-grade tumors, and are generally considered the least aggressive in behavior. Conversely, the cells of Grade 3 or Grade 4 tumors are usually poorly differentiated or undifferentiated high-grade tumors, and are generally the most aggressive in behavior.

Furthermore, the grading system used to assess a tumor may be different for each type of cancer. In general, tumor grade is a system used to classify cancer cells in terms of how abnormal they look under a microscope and how quickly the tumor is likely to grow and spread. Tumor grade may be determined by many factors, including the structure and growth pattern of the cells. Accordingly, the specific factors used to determine tumor grade may vary with each type of cancer.

The term “tumor stage” or “cancer stage” is intended to refer to the extent or severity of the cancer, based on factors such as the location of the primary tumor, tumor size, number of tumors, and lymph node involvement (spread of cancer into lymph nodes).

The term “cancer cell-containing sample” includes a sample of cells, tissue, or fluid taken from the diseased area of a subject with cancer. The cancer cell-containing sample may also include cancer cells or cell lines kept in culture. The cancer cell-containing sample may also include a fluid, e.g., saline, that is introduced into the subject, and then removed from the subject for analysis. The cancer cell-containing sample may further include tumor cells isolated from blood peripheral to the diseased area.

The term “normal tissue sample” includes a sample of cells, tissue, or fluid taken from a disease-free subject or from a disease-free area of a subject with cancer or a disease-free area of the cancer containing tissue of a subject with cancer. The normal tissue sample may also include normal cells kept in culture. Furthermore, the normal tissue sample may also include a fluid that was introduced into the subject, e.g., saline, and then removed from the subject for analysis.

The term “reference sample” includes a sample corresponding to normal tissue or cells take from the same individual or a different individual. For example, the reference sample may be taken from a disease-free area of the cancer containing tissue in the subject of interest or the reference sample may be taken from disease-free tissue of the subject of interest that does not correspond to the diseased-tissue. In another example, the reference sample may be taken from the tissue of a disease-free subject, either from tissue that corresponds to the diseased-tissue of the subject of interest or other normal tissue of the disease-free subject.

The term “reference level” refers to a control level of expression of a nucleotide sequence or polypeptide used to evaluate a test level of expression of a nucleotide sequence or polypeptide in a cancer cell-containing sample of a patient. For example, when the level of NOL3 in the cancer cell-containing sample of a patient is higher than the reference level of NOL3, the cells will be considered to have a high level of expression, or overproduction, of NOL3. Conversely, when the level of NOL3 in the cancer cell-containing sample of a patient are equivalent or lower than the reference level, the cells will be considered to have a normal or low level of expression of NOL3. In one aspect, the reference level may be determined by assaying the level of expression of the nucleotide sequence or polypeptide of interest in the reference sample.

The term “NOL3” refers to nucleolar protein 3 (apoptosis repressor with CARD domain). The term “NOL3” includes ARC, MYC, MYP, NOP, and NOP30. Preferably, the term “NOL3” refers to NOL3 mRNA. The term “ARC” refers to apoptosis repressor with CARD domain, the term ARC may also refer to nucleolar protein 3 (apoptosis repressor with CARD domain).

The term “NOL3” refers to NOL3 and/or ARC. Preferably, the term “NOL3” refers to NOL3 mRNA and/or NOL3 polypeptide.

The term “level of NOL3 mRNA” refers to the expression level of NOL3 mRNA in the sample of interest. In one aspect, the level of NOL3 mRNA may be assayed by a technique selected from the group including Northern blot, RT-PCT, Quantitative PCR (QPCR), non-PCR amplification methods (e.g., strand displacement amplification (SDA), rolling-circle amplification (RCA), multiple-displacement amplification (MDA), transcription meditated amplification (TMA), and nucleic acid sequence based amplification (NASBA)), Luminex bead analysis, in situ hybridization, and gene expression microarray analysis.

The term “slight increase in NOL3 mRNA” refers to a slight increase in the expression level of mRNA in a sample of interest when compared to a reference sample. For example, the slight increase in NOL3 mRNA may correspond to the difference in NOL3 mRNA expression levels between a reference sample and the expression level observed in a sample from a grade III tumor.

The term “moderate increase in NOL3 mRNA” refers to a moderate increase in the expression level of mRNA in a sample of interest when compared to a reference sample. For example, a moderate increase in NOL3 mRNA may correspond to the difference in NOL3 mRNA expression levels between a reference sample and the expression level observed in a sample from a grade IV tumor.

The term “large increase in NOL3 mRNA” refers to a large increase in the expression level of mRNA in a sample of interest when compared to a reference sample. For example, a large increase in NOL3 mRNA may correspond to the difference in NOL3 mRNA expression levels between a reference sample and the expression level observed in a recurrent tumor.

The term “level of NOL3 polypeptide” refers to the expression level of NOL3 polypeptide in the sample of interest. In one aspect, the level of NOL3 polypeptide may be assayed by a technique selected from the group including western blot, immunohistochemistry, indirect immunofluorescence, direct immunofluorescence, intracellular flow cytometry, enzyme-linked immunosorbent assay (ELISA), and antibody microarray analysis.

The term “slight increase in NOL3 polypeptide” refers to a slight increase in the polypeptide expression level in a sample of interest when compared to a reference sample. For example, the slight increase in NOL3 polypeptide may correspond to the difference in NOL3 polypeptide expression levels between a reference sample and the expression level observed in a sample from a grade 111 tumor.

The term “moderate increase in NOL3 polypeptide” refers to a moderate increase in the polypeptide expression level in a sample of interest when compared to a reference sample. For example, a moderate increase in NOL3 polypeptide may correspond to the difference in NOL3 polypeptide expression levels between a reference sample and the expression level observed in a sample from a grade IV tumor.

The term “large increase in NOL3 polypeptide” refers to a large increase in the polypeptide expression level in a sample of interest when compared to a reference sample. For example, a large increase in NOL3 polypeptide may correspond to the difference in NOL3 polypeptide expression levels between a reference sample and the expression level observed in a recurrent tumor.

The term “level of survivin” refers to the expression level of survivin mRNA or polypeptide. In one aspect, the level of survivin mRNA may be assayed by a technique selected from the group including Northern blot, RT-PCR, Quantitative PCR (QPCR), in situ hybridization, and gene expression microarray analysis. In another aspect, the level of survivin polypeptide may be assayed by a technique selected from the group including western blot, immunohistochemistry, indirect immunofluorescence, direct immunofluorescence, intracellular flow cytometry, enzyme-linked immunosorbent assay (ELISA), and antibody microarray analysis.

The term “higher level of NOL3” refers to an increase in the expression level of NOL3 polypeptide in the sample of interest when compared to a reference sample.

The term “survival”, refers to the act or fact of living. The term “disease-free survival” is intended to refer to the lack of tumor recurrence and/or spread and the fate of a patient after diagnosis, for example, a patient who is alive without tumor recurrence. The phrase “overall survival” refers to the fate of the patient after diagnosis, regardless of whether the patient has a recurrence of the tumor.

The term “IAP inhibitor” refers to any compound that inhibits the activity of a member of the TAP family of proteins. Such compounds may include, for example, small molecules, polypeptides (i.e., Smac mimetic peptides), RNA interference molecules targeting IAP proteins (e.g., siRNA, shRNA, miRNA or antisense RNA), anti-IAP antibodies and agents that inhibits IAPs. Preferably, the IAP inhibitor is LBW-242. In another preferred embodiment, the IAP inhibitors that can be used in the instant invention, and methods of making them, are disclosed in WO 2005/097791 and WO 2008/016893, both herein incorporated by reference in their entirety.

The term “anti-cancer agent” includes compounds which inhibit or suppress the growth of cancer cells. An anti-cancer agent may also include compounds that destroy cancer cells or interfere with cell division, monoclonal antibodies that bind proteins on the cell surface, peptides that bind cell surface receptors, interferons or cytokines which induce an immune response, vaccines which generate an immune response, hormones or compounds that block certain hormones involved in cancer, compounds that inhibit or prevent the growth of new blood vessels, (i.e., angiogenesis inhibitors), agents that damage DNA (e.g., alkylating agents, for example, cisplatin, carboplatin, and oxaloplatin; anti-metabolites; and topoisomerase inhibitors), and compounds with anti-cancer properties (e.g., taxanes, vinca alkaloids, and plant alkaloids). The term “anti-cancer agent” also includes radiation therapy. An anti-cancer agent may also include an agent specific for deregulated proteins of cancer cells, such as an inhibitor of receptor tyrosine kinases, preferably imatinib.

The term “subject” includes humans, and non-human animals amenable to therapy, e.g., preferably mammals and animals susceptible to cancer, such as non-human primates, transgenic animals, dogs, cats, horses, and cows. The term “subject” also includes patients, more preferably cancer patients. The term “cancer patient” includes humans, and non-human animals that have cancer.

The term “prognosis” is intended to denote the prediction of how a patients disease will progress, whether there is a chance for recovery and how a patient may respond to treatment.

The term “responsiveness” refers to a positive reaction by a subject undergoing treatment with an anti-cancer agent, an IAP inhibitor or an anti-cancer agent and an IAP inhibitor. The term “positive reaction” includes any response that is not negative.

The term “predicting responsiveness” refers to the ability to foretell or infer whether a subject will respond in a positive manner, (e.g., whether a patient will be responsive) or a negative manner.

The term “treatment” refers to a process, manner or regimen which allows for medicinal or surgical care for an illness or injury in a subject. In certain embodiments, the treatment comprises diminishing or alleviating at least one symptom directly or indirectly associated with or caused by cancer. For example, treatment can be diminishment of one or several symptoms of cancer or complete eradication of cancer.

The term “treatment regimen” refers to a regulated course of treatment intended to preserve or restore health, or to attain some result, e.g., inhibit or suppress tumor growth. In one embodiment the treatment regimen may include administering an anti-cancer agent to a cancer patient, preferably, imatinib. In another embodiment, the treatment regimen may include administering an IAP inhibitor to a cancer patient, preferably LBW-242. In a further embodiment, the treatment regimen may include administering an anti-cancer agent and an IAP inhibitor to a cancer patient, preferably imatinib and LBW-242.

Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Although methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present invention, suitable methods and materials are described below. All publications, patent applications, patents, and other references mentioned herein are incorporated by reference in their entirety. In case of conflict, the present specification, including definitions, will control. In addition, the materials, methods, and examples are illustrative only and are not intended to be limiting.

Various aspects of the invention are described in further detail in the following subsections.

Prediction of Responsiveness to Therapy for Cancer

In one aspect, the invention pertains to a method for predicting the prognosis for survival of a cancer patient. Typically, the method comprises assaying the level of NOL3/NOL3 in a cancer cell-containing sample from a cancer patient and comparing the level of NOL3 to a reference level, and predicting the prognosis for survival of the patient based on the levels of NOL3.

A variety of growth factor receptors are instrumental in the tumorigenesis of gliomas and have been validated as therapeutic targets. Malignant gliomas often exhibit over-expression of both platelet derived growth factor (PDGF) and platelet derived growth factor receptor (PDGFR), which contribute to tumor progression via an autocrine or paracrine loop (Fleming et al., Cancer Res. 52, 4550-4553, 1992.; Guha et al., Int. J. Cancer 60, 168-173, 1995.; Hermanson et al., Cancer Res. 52, 3213-3219, 1992.). Antagonism of PDGFR with the tyrosine kinase inhibitor imatinib (STI571, Gleevec) in both in vitro and in vivo glioma models has demonstrated successful inhibition of tumor growth (Kilic et al., Cancer Res. 60, 5143-5150, 2000.).

In addition, the Inhibitor of Apoptosis Proteins (IAPs) have been shown to be highly expressed in malignant gliomas. The IAPs represent the final molecular blockade preventing apoptosis by inhibiting the activity of caspases 3, 7 and 9. The IAP survivin has been identified in the majority of gliomas where its levels correlated inversely with prognosis.

A variety of anti-apoptotic mechanisms render glioma cells chemo- and radio-resistant, and it has been hypothesized that these anti-apoptotic mechanisms likewise confer resistance to RTK inhibition. The anti-apoptotic protein NOL3 was found to be highly expressed in malignant gliomas and its expression correlates with poor survival. It has been demonstrated that RTK inhibition activates the apoptotic cascade by decreasing the expression of NOL3, but does not result in downstream caspase activation. Small molecule blockade of the IAPs in combination with RTK inhibition results in caspase activation and apoptosis, and has synergistic anti-tumor efficacy in vitro and in vivo in orthotopic glioma models.

In one aspect, the method of the present invention relates to determining the prognosis for survival of a cancer patient. In one embodiment, the method includes measuring a level of NOL3 expression in a cancer cell-containing sample from a cancer patient and comparing the level of NOL3 expression in the sample to a reference level of NOL3. For example, a higher level of NOL3 in the sample relative to the reference level correlates with decreased survival of the patient, and an equivalent or lower level of NOL3 relative to the reference sample correlates with increased survival of the patient.

In another aspect, the method of the present invention relates to determining the prognosis for survival of a cancer patient by measuring the level of NOL3 and measuring the level of survivin in a cancer cell-containing sample from the patient. Furthermore, the method includes comparing the level of NOL3 and survivin expression to a reference level of NOL3 expression and a reference level of survivin expression. For example, a higher level of NOL3 and a higher level of survivin relative to the reference level correlates with decreased survival of the patient, and an equivalent or lower level of NOL3 and an equivalent or lower level of survivin relative to the reference level correlates with increased survival.

In one aspect, the method of the present invention provides a method of predicting responsiveness to an anti-cancer agent in a subject having cancer, wherein the cancer agent reduces the expression of NOL3, the method comprising: measuring the level of NOL3 expression in a cancer cell-containing sample from the subject and comparing the level of NOL3 in the sample to a reference level of NOL3. For example, a higher level of NOL3 expression relative to the reference level predicts responsiveness of the patient to the anti-cancer agent. Also, for example, a higher level of NOL3 expression relative to the reference level predicts responsiveness of the subject to the anti-cancer agent administered in combination with an IAP inhibitor.

In another aspect, the method of the present invention includes predicting the responsiveness of a subject having cancer to an IAP inhibitor by measuring the expression level of NOL3 in a cancer cell-containing sample and comparing the level of NOL3 in the sample to a reference level of NOL3. In one embodiment, an equivalent or lower level of NOL3 expression relative to the reference sample predicts responsiveness of the subject to an IAP inhibitor.

In a one aspect, the present invention provides a method for selecting a subject having cancer for a treatment regimen by the method comprising: measuring the level of NOL3 in a cancer cell containing sample from the subject, comparing the level of NOL3 expression in the sample to the reference level of NOL3 and selecting subjects having elevated NOL3 expression for a treatment regimen including a NOL3 inhibitor. Preferably, the subjects having elevated NOL3 expression are selected for a treatment regimen comprising an agent that reduces NOL3 activity and an IAP inhibitor. In one embodiment, the selected subject has an equivalent or lower level of NOL3 expression relative to the reference sample and is selected for a treatment regimen comprising an IAP inhibitor.

In one aspect, the method of the present invention provides a means for diagnosing the grade or stage of a tumor in a subject having cancer. In one embodiment the method includes measuring the level of NOL3 expression in a cancer cell-containing sample from the subject and comparing the level of NOL3 in the sample to a reference level. For example, a higher level of NOL3 relative to the reference sample correlates with worsening tumor grade.

The methods of the present invention may be used to predict prognosis for survival of a patient having any cancer. Examples of cancers that are embodied by the present invention, include but are not limited to breast, brain, ovarian, colorectal, gastric, prostate, testicular, uterine, cervical, pancreatic, skin, colon, stomach, esophagus, bladder, lung, and small cell lung cancer. In one embodiment, the subject suffers from a glioma; for example, an astrocytoma, ependymoma, oligodendroglioma, mixed glioma, and glioblastoma multiforme. In another embodiment, the subject suffers from a carcinoma; for example, ovarian carcinoma, colorectal carcinoma, and small cell lung carcinoma. In another embodiment, the subject suffers from a hematologic malignancy; for example, acute leukemia, chronic leukemia, multiple myeloma, or lymphoma.

In a further embodiment the subject suffers from a sarcoma; for example, osteosarcoma, chondrosarcoma, leiomyosarcoma, gastrointestinal stromal tumor (GIST). Ewing's sarcoma, Askin's tumor, malignant hemangioendothelioma, malignant schwannoma, and soft tissue sarcoma (e.g., alveolar soft part sarcoma, angiosarcoma, cystosarcoma phylloides, dermatofibrosarcoma, desmoid tumor, desmoplastic small round cell tumor, epithelioid sarcoma, extraskeletal chondrosarcoma, extraskeletal osteosarcoma, fibrosarcoma, hemangiopericytoma, hemangiosarcoma, Kaposi's sarcoma, liposarcoma, lymphangiosarcoma, lymphosarcoma, malignant fibrous histiocytoma, neurofibrosarcoma, rhabdomyosarcoma, and synovial sarcoma).

In the method of the invention for predicting the prognosis for survival of a cancer patient, the level of expression of NOL3 (e.g., NOL3 mRNA) can be assayed in the subject using techniques well established in the art. In a preferred embodiment, the expression level of NOL3 mRNA in the subject is assayed by obtaining a cancer cell-containing sample from the subject and detecting the level of NOL3 mRNA. Additionally or alternatively, the level of expression of NOL3 polypeptide can be assayed in the subject using techniques well established in the art. Preferably, the expression level of NOL3 polypeptide in the subject is assayed by obtaining a cancer cell-containing sample from the subject and detecting the level of NOL3 polypeptide. Furthermore, the expression level of NOL3 mRNA and/or NOL3 polypeptide can be assayed in a reference sample using techniques well established in the art. Preferably, the expression level of NOL3 mRNA and/or NOL3 polypeptide is assayed by obtaining a disease free reference sample from the subject of interest or a disease free subject and detecting the level of NOL3 mRNA and/or NOL3 polypeptide in the sample.

For example, an assay for detecting the levels of mRNA in a sample may be selected from the group including Northern blot, RT-PCR, Quantitative PCR (QPCR), in situ hybridization, and gene expression microarray analysis. In an exemplary embodiment of these aspects, a nucleotide probe that hybridizes to NOL3 mRNA can be used to detect NOL3 mRNA. In another embodiment of these aspects, a nucleotide probe which hybridizes to survivin mRNA may be used to detect survivin mRNA. Also for example, an assay for detecting the levels of a polypeptide in a sample may be selected from the group including Western blot, immunohistochemistry, indirect immunofluorescence, enzyme-linked immunosorbent assay (ELISA), and antibody microarray analysis. In an exemplary embodiment of these aspects, an antibody that binds NOL3 polypeptide may be used to detect NOL3 polypeptide. In another embodiment of these aspects, an antibody that binds survivin polypeptide may be used to detect survivin polypeptide.

The specific examples described above for detecting the expression levels of mRNA and/or a polypeptide are representative examples and are not intended to be limiting. Other suitable approaches for assaying the expression level of mRNA and/or a polypeptide are known in the art. It will be readily understood by the ordinarily skilled artisan that essentially any technical means established in the art for detecting mRNA and/or polypeptide levels in a sample can be adapted to the detection of NOL3 and/or survivin as discussed herein and applied in the methods of the current invention for predicting patient outcome.

Selection and Use of a Compound with Anti-Cancer Properties

Given the observation that the increase in NOL3 in cancer patients influences the responsiveness of the subject to therapy, one can select an appropriate compound with anti-cancer properties for the treatment of a subject based on the level of NOL3 in the subject. Accordingly, in one aspect, the above-described method for predicting prognosis for survival of a cancer patient further comprises selecting a compound with anti-cancer properties.

A compound with anti-cancer properties may include compounds that inhibit or suppress the growth of cancer cells. A compound with anti-cancer properties can also include an anti-cancer agent, compounds that destroy cancer cells or interfere with cell division, monoclonal antibodies that bind proteins on the cell surface, peptides that bind cell surface receptors, interferons or cytokines which induce an immune response, vaccines which generate an immune response, hormones or compounds that block certain hormones involved in cancer, compounds that inhibit or prevent the growth of new blood vessels, i.e., angiogenesis inhibitors. A compound with anti-cancer properties may also include an agent specific for deregulated proteins of cancer cells, such as an inhibitor of receptor tyrosine kinases, preferably imatinib.

In one aspect, the method of the present invention includes identifying a compound as an anti-cancer agent. For example, a cell line expressing NOL3 is treated with a compound and the change in NOL3 expression is determined, and a compound that reduces the level of NOL3 expression is identified as an anti-cancer agent. Preferably, the method of the present invention relates to the treatment of cancer by administering the identified compound of this aspect alone or in combination with an IAP inhibitor.

The present invention provides methods for identifying a compound as an anti-cancer agent. In one aspect, such a method includes treating a cell line expressing NOL3 with a compound; assaying for a change in NOL3 expression after treatment with the compound; and identifying a compound that reduces the level of NOL3 as an anti-cancer agent.

In one embodiment, the present invention pertains to methods of treating a subject with cancer. For example, the subject may be treated with the anti-cancer agent identified by the method of the instant application. Alternatively or additionally, the subject may be treated with other anti-cancer agents, i.e., biologic agents and/or other therapeutic anti-cancer agents, such as traditional chemotherapeutic agents, radiotherapeutic agents and/or inhibitors of receptor tyrosine kinases.

Preferably, the methods of the present invention pertain to the treatment of a cancer patient with an inhibitor of receptor tyrosine kinases. In one embodiment, treatment with an inhibitor of receptor tyrosine kinases results in the antagonism of epidermal growth factor receptor (EGFR), EGFRvIII, and/or insulin-like growth factor-1 receptor (IGF1R). In a preferred embodiment, treatment with an inhibitor of receptor tyrosine kinases results in the antagonism of platelet derived growth factor receptor (PDGFR).

In a preferred embodiment, the receptor tyrosine kinase inhibitor is selected from the group including imatinib, AMN107, AEW541 and PKI166.

In another embodiment, the present invention pertains to the treatment of a cancer patient with an anti-cancer agent and an agent that inhibits the inhibitor of apoptosis proteins (IAPs). In a preferred embodiment the inhibitor of IAPs is LBW242.

In another preferred embodiment, the present invention relates to the treatment of neoplasms, comprising the combination of a growth factor receptor inhibitor and an inhibitor of IAPs disclosed in WO 2008/109057, incorporated herein by reference in its entirety.

Preferably, the present invention pertains to the treatment of a cancer patient with an inhibitor of receptor tyrosine kinases in combination with an inhibitor of IAPs. More preferably, the present invention pertains to the treatment of a cancer patient with AMN107 and LBW242. Most preferably, the present invention pertains to the treatment of a cancer patient with imatinib and LBW242.

In one embodiment, the inhibitor of receptor tyrosine kinases is administered in doses that range from 0.1 μM to greater than or equal to 100 μM. For example, the dose may be 0.1 μM, 0.5 μM, 1.0 μM, 1.5 μM, 2.0 μM, 2.5 μM, 3.0 μM, 3.5 μM, 4.0 μM, 4.5 μM, 5.0 μM, 10.0 μM, 15.0 μM, 20.0 μM, 25.0 μM, 30.0 μM, 40.0 μM, 50.0 μM, 60.0 μM, 70.0 μM, 80.0 μM, 90.0 μM to greater than about 100.0 μM or any incremental value thereof. It is to be understood that all values and ranges between these values and ranges are meant to be encompassed by the present invention. In some embodiments the inhibitor of receptor tyrosine kinases is administered at a dose of 2.5 μM. In other embodiments, the inhibitor of receptor tyrosine kinases is administered at a dose of 10 μM. In still other embodiments, the inhibitor of receptor tyrosine kinases is administered at a dose of greater than about 20.0 μM.

In an exemplary embodiment, the inhibitor of receptor tyrosine kinases is selected from the group including AMN107, AEW541 and PKI166. In a preferred exemplary embodiment, the inhibitor of receptor tyrosine kinases is imatinib.

In one embodiment, the inhibitor of IAPs is administered in doses that range from 1.0 μM to greater than or equal to 500 μM. For example, the dose may be 1.0 μM, 5.0 μM, 10.0 μM, 15.0 μM, 20.0 μM, 25.0 μM, 30.0 μM, 35.0 μM, 40.0 μM, 45.0 μM, 50.0 μM, 60.0 μM, 70.0 μM, 80.0 μM, 90.0 μM, 100.0 μM, 150.0 μM, 200.0 μM, 250.0 μM, 300.0 μM, 350.0 μM, 400.0 μM, 450.0 μM, to greater than about 500.0 μM or any incremental value thereof. It is to be understood that all values and ranges between these values and ranges are meant to be encompassed by the present invention. In some embodiments the inhibitor of IAPs is administered at a dose of 50.0 μM. In other embodiments, the inhibitor of IAPs is administered at a dose of 60.0 μM. In still other embodiments, the inhibitor of IAPs is administered at a dose of greater than about 100.0 μM.

In a preferred exemplary embodiment, the inhibitor of IAPs is LBW242.

In another embodiment, the compounds discussed herein, i.e., inhibitors of receptor tyrosine kinases and inhibitors of IAPs, are administered at a concentration in the range from about 1 mg/kg to greater than about 500 mg/kg. For example, the concentration may be 1.0 mg/kg, 5.0 mg/kg, 10.0 mg/kg, 15.0 mg/kg, 20.0 mg/kg, 25.0 mg/kg, 30.0 mg/kg, 35.0 mg/kg, 40.0 mg/kg, 45.0 mg/kg, 50.0 mg/kg, 60.0 mg/kg, 70.0 mg/kg, 80.0 mg/kg, 90.0 mg/kg, 100.0 mg/kg, 150.0 mg/kg, 200.0 mg/kg, 250.0 mg/kg, 300.0 mg/kg, 350.0 mg/kg, 400.0 mg/kg, 450.0 mg/kg, to greater than about 500.0 mg/kg or any incremental value thereof. It is to be understood that all values and ranges between these values and ranges are meant to be encompassed by the present invention. In some embodiments the inhibitor of IAPs is administered at a concentration of 50.0 mg/kg. In other embodiments, the inhibitor of IAPs is administered at a concentration of 100.0 mg/kg. In still other embodiments, the inhibitor of IAPs is administered at a concentration of greater than about 500.0 mg/kg.

In a preferred exemplary embodiment, the inhibitor of IAPs is LBW242.

In an exemplary embodiment, the inhibitor of receptor tyrosine kinases is selected from the group including AMN107, AEW541 and PK1166. In a preferred exemplary embodiment, the inhibitor of receptor tyrosine kinases is imatinib.

For administration to a subject, a therapeutic agent typically is formulated into a pharmaceutical composition containing the therapeutic agent and a pharmaceutically acceptable carrier. Therapeutic compositions typically must be sterile and stable under the conditions of manufacture and storage. Pharmaceutical compositions also can be administered in combination therapy, i.e., combined with other agents, such as other biologic agents and/or other therapeutic agents, such as traditional chemotherapeutic agents, radiotherapeutic agents and/or inhibitors of receptor tyrosine kinases for the treatment of cancer.

The term, “pharmaceutically acceptable carrier” includes any and all solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic and absorption delaying agents, and the like that are physiologically compatible. Preferably, the carrier is suitable for intravenous, intramuscular, subcutaneous, parenteral, spinal or epidermal administration (e.g., by injection or infusion). Depending on the route of administration, the active compound may be coated in a material to protect the compound from the action of acids and other natural conditions that may inactivate the compound.

The pharmaceutical compositions may include one or more pharmaceutically acceptable salts. A “pharmaceutically acceptable salt” refers to a salt that retains the desired biological activity of the parent compound and does not impart any undesired toxicological effects (see e.g., Berge, S. M., et al. (1977) J. Pharm. Sci. 66:1-19). Examples of such salts include acid addition salts and base addition salts. Acid addition salts include those derived from nontoxic inorganic acids, such as hydrochloric, nitric, phosphoric, sulfuric, hydrobromic, hydroiodic, phosphorous and the like, as well as from nontoxic organic acids such as aliphatic mono- and dicarboxylic acids, phenyl-substituted alkanoic acids, hydroxy alkanoic acids, aromatic acids, aliphatic and aromatic sulfonic acids and the like. Base addition salts include those derived from alkaline earth metals, such as sodium, potassium, magnesium, calcium and the like, as well as from nontoxic organic amines, such as N,N′-dibenzylethylenediamine, N-methylglucamine, chloroprocaine, choline, diethanolamine, ethylenediamine, procaine and the like.

A pharmaceutical composition also may include a pharmaceutically acceptable anti-oxidant. Examples of pharmaceutically acceptable antioxidants include: (1) water soluble antioxidants, such as ascorbic acid, cysteine hydrochloride, sodium bisulfate, sodium metabisulfite, sodium sulfite and the like; (2) oil-soluble antioxidants, such as ascorbyl palmitate, butylated hydroxyanisole (BHA), butylated hydroxytoluene (BHT), lecithin, propyl gallate, alpha-tocopherol, and the like; and (3) metal chelating agents, such as citric acid, ethylenediamine tetraacetic acid (EDTA), sorbitol, tartaric acid, phosphoric acid, and the like.

Examples of suitable aqueous and nonaqueous carriers that may be employed in the pharmaceutical compositions include water, ethanol, polyols (such as glycerol, propylene glycol, polyethylene glycol, and the like), and suitable mixtures thereof, vegetable oils, such as olive oil, and injectable organic esters, such as ethyl oleate. Proper fluidity can be maintained, for example, by the use of coating materials, such as lecithin, by the maintenance of the required particle size in the case of dispersions, and by the use of surfactants.

These compositions may also contain adjuvants such as preservatives, wetting agents, emulsifying agents and dispersing agents. Prevention of presence of microorganisms may be ensured both by sterilization procedures and by the inclusion of various antibacterial and antifungal agents, for example, paraben, chlorobutanol, phenol sorbic acid, and the like. It may also be desirable to include isotonic agents, such as sugars, sodium chloride, and the like into the compositions. In addition, prolonged absorption of the injectable pharmaceutical form may be brought about by the inclusion of agents which delay absorption such as aluminum monostearate and gelatin.

Pharmaceutically acceptable carriers include sterile aqueous solutions or dispersions and sterile powders for the extemporaneous preparation of sterile injectable solutions or dispersion. The use of such media and agents for pharmaceutically active substances is known in the art. Except insofar as any conventional media or agent is incompatible with the active compound, use thereof in the pharmaceutical compositions of the invention is contemplated. Supplementary active compounds can also be incorporated into the compositions.

A therapeutic agent of the present invention can be administered via one or more routes of administration using one or more of a variety of methods known in the art. As will be appreciated by the skilled artisan, the route and/or mode of administration will vary depending upon the desired results. A preferred route of administration, particularly for therapeutic agents, is by intravenous injection or infusion. Other preferred routes of administration include intramuscular, intradermal, intraperitoneal, subcutaneous, spinal or other parenteral routes of administration, for example by injection or infusion. The phrase “parenteral administration” as used herein means modes of administration other than enteral and topical administration, usually by injection, and includes, without limitation, intravenous, intramuscular, intraarterial, intrathecal, intracapsular, intraorbital, intracardiac, intradermal, intraperitoneal, transtracheal, subcutaneous, subcuticular, intraarticular, subcapsular, subarachnoid, intraspinal, epidural and intrasternal injection and infusion. Alternatively, a therapeutic agent of the invention can be administered via a non-parenteral route, such as a topical, epidermal or mucosal route of administration, for example, intranasally, orally, vaginally, rectally, sublingually or topically.

In a preferred embodiment, the subject to be treated with the anti-cancer agent is a human subject, more preferably a human subject that suffers from cancer. Examples of cancers that are embodied by the present invention, include but are not limited to breast, brain, ovarian, colorectal, gastric, prostate, testicular, uterine, cervical, pancreatic, skin, colon, stomach, esophagus, bladder, lung, and small cell lung cancer. In one embodiment, the subject suffers from a glioma; for example, an astrocytoma, ependymoma, oligodendroglioma, mixed glioma, and glioblastoma multiforme. In another embodiment, the subject suffers from a carcinoma; for example, ovarian carcinoma, colorectal carcinoma, and small cell lung carcinoma. In another embodiment, the subject suffers from a hematologic malignancy; for example, acute leukemia, chronic leukemia, multiple myeloma, or lymphoma.

Kits of the Invention

In another aspect, the present invention pertains to kits for carrying out the methods of the invention. For example, in one embodiment, the invention provides a kit for predicting responsiveness to an anti-cancer agent in a subject having cancer, wherein the anti-cancer agent reduces the expression or activity of NOL3. In one embodiment, the kit includes:

a) means for detecting the level of NOL3 expression in a cancer cell containing sample; and

b) instructions for use of the kit to predict responsiveness to an anti-cancer agent in a subject having cancer.

In a preferred embodiment, the kit of the present invention further includes an anti-cancer agent. In another preferred embodiment, the kit of the present invention may further comprise an IAP inhibitor.

In one embodiment, the present invention provides a kit for predicting the responsiveness of a subject having cancer to an IAP inhibitor, the kit includes:

a) means for detecting the level of NOL3 expression in a cancer cell containing sample from the subject; and

b) instructions for use of the kit to predict responsiveness to an IAP inhibitor in a subject having cancer.

In a preferred embodiment, the kit of the present invention further includes an IAP inhibitor. In another preferred embodiment, the kit of the present invention may further comprise an anti-cancer agent.

In an exemplary embodiment, the means for detecting the expression level of target mRNA in a subject having cancer may include a nucleic acid preparation. This nucleic acid preparation includes at least one, and may include more than one nucleic acid probe or primer, the sequence of which is designated such that the nucleic acid preparation hybridizes to the mRNA of interest. A preferred nucleic acid preparation includes at least one labeled probe so that the target mRNA can be detected. A more preferred nucleic acid preparation includes two or more primers that allow for amplification of the target mRNA. For example, suitable probes and primers comprise a sequence which hybridizes to NOL3 mRNA. Also for example, suitable probes and primers comprise a sequence which hybridizes to survivin mRNA.

Furthermore, the means for detecting the expression level of a target polypeptide in a subject having cancer comprises a reagent that detects a gene product in a cancer cell containing sample from the subject of interest and/or a reference sample. A non-limiting example of such a reagent is a monoclonal antibody specific for NOL3. Another non-limiting example of such a reagent is a monoclonal antibody specific for survivin.

The means for assaying the presence of NOL3 or survivin can also include, for example, buffers or other reagents for use in an assay for evaluating the expression level of NOL3 or survivin. The instructions can be, for example, printed instructions for performing the assay for evaluating the expression level of NOL3 or survivin.

In another example, the kit can further comprise an anti-cancer agent for treating cancer in a subject.

In a preferred embodiment, the kit includes means for detecting the expression level of NOL3 in a subject as a predictor for responsiveness to an anti-cancer agent. In this embodiment, the instructions can instruct the end user of the kit that the presence of an increased level of NOL3 relative to the reference level predicts responsiveness of the subject to the anti-cancer agent. Also in this embodiment, the instructions can instruct the end user of the kit that the presence of an increased level of NOL3 relative to the reference level predicts responsiveness of the subject to the anti-cancer agent administered in combination with an IAP inhibitor.

In another preferred embodiment, the kit includes means for detecting the level of NOL3 in a subject as a predictor for responsiveness to an IAP inhibitor. In this embodiment, the instructions can instruct the end user of the kit that an equivalent or lower level of NOL3 relative to the reference level predicts responsiveness of the subject to an IAP inhibitor.

In another embodiment, the kit includes means for detecting the expression level of NOL3 in a subject as a means for determining the prognosis for survival of a cancer patient. In this embodiment, the instructions can instruct the end user of the kit that the presence of an increased level of NOL3 relative to the reference level correlates with decreased survival of the patient. Additionally or alternatively, the instructions can instruct the end user of the kit that equivalent or lower levels of NOL3 relative to the reference level correlate with increased survival of the patient.

Additionally, the kit may include means for detecting the expression level of survivin in a subject as a means for determining the prognosis for survival of a cancer patient. In this embodiment, the instructions can instruct the end user of the kit that the presence of an increased level of survivin relative to the reference sample correlates with decreased survival of the patient. Additionally or alternatively, the instructions can instruct the end use of the kit that equivalent or lower levels of survivin relative to the reference levels correlates with increased survival of the patient.

In another aspect, the kit of the present invention includes means for diagnosing the grade or stage of a tumor in a subject. In this aspect, the instructions can instruct the end user of the kit that an increased level of NOL3 relative to the reference level correlates with worsening grade or stage of the tumor. For example, a slight increase in NOL3 correlates with a grade III tumor, a moderate increase in NOL3 correlates with a grade IV tumor, and a large increase in NOL3 correlates with a recurrent tumor.

In a another aspect, the kit of the present invention includes means for selecting a subject having cancer for a treatment regimen. In this aspect, the instructions can instruct the end user of the kit that a subject having a higher level of NOL3 relative to the reference level is selected for a treatment regime comprising an agent that reduces the expression or activity of NOL3. Also, the instructions may instruct the end user of the kit that a subject having a higher level of NOL3 subject may be selected for a treatment regimen additionally comprising an IAP inhibitor. Furthermore, the kit may comprise the agent used in the treatment regimen to reduce the activity of NOL3 and/or an IAP inhibitor.

In another aspect, the kit of the present invention includes means for selecting a subject having cancer for a treatment regimen. In this aspect, the instructions can instruct the end user of the kit that a subject having an equivalent or lower levels of NOL3 relative to the reference level is selected for a treatment regimen including an IAP inhibitor.

In still other embodiments, the kit may include a means for identifying a compound as an anti-cancer agent. In this embodiment, the kit may comprise a cell line expressing NOL3 and/or a compound for use in treating the cell line. Furthermore, the instructions can instruct the end user of the kit that a compound that reduces the level of NOL3 expression may be identified as an anti-cancer agent.

Preferably, the kit is designed for use with a human subject, such as a human subject suffering from cancer. Examples of cancers that are embodied by the present invention, include but are not limited to breast, brain, ovarian, colorectal, gastric, prostate, testicular, uterine, cervical, pancreatic, skin, colon, stomach, esophagus, bladder, lung, and small cell lung cancer. In one embodiment, the subject suffers from a glioma; for example, an astrocytoma, ependymoma, oligodendroglioma, mixed glioma, and glioblastoma multiforme. In another embodiment, the subject suffers from a carcinoma; for example, ovarian carcinoma, breast carcinoma, prostate carcinoma, colorectal carcinoma, and small cell lung carcinoma. In another embodiment, the subject suffers from a hematologic malignancy; for example, acute leukemia, chronic leukemia, multiple myeloma, or lymphoma.

This invention is further illustrated by the following examples, which should not be construed as limiting. The contents of all references, patents and published patent applications cited throughout this application are incorporated herein by reference.

EXAMPLES Example 1 PDGFR and IAP Inhibition Synergistically Inhibits Glioma Cell Growth

It has been proposed that cancer cells exist in a state of dynamic tension with a constant burden of pro-apoptotic signals counterbalanced by heightened expression of anti-apoptotic proteins. The IAPs constitute a final blockade of apoptosis through sequestration of caspase-3, -7, and -9 (FIG. 1A). Upon mitochondrial permeabilization, release of Smac/DIABLO into the cytoplasm results in binding to, and inactivation of, IAPs. Since IAPs are overexpressed in gliomas, it is possible that blockade of IAPs alone may be sufficient to shift the balance towards apoptosis (FIG. 1A). The small molecule LBW242 binds to the BIR3 domain of IAPs, and blocks their ability to sequester caspases. To confirm that LBW242 does in fact effectively function as a Smac mimetic, a FRET based competition assay that measured the ability of LBW242 to compete with Smac for binding to the BIR3 domain of XIAP was performed. LBW242 inhibited the interaction of full-length Smac to XIAP in a well-behaved sigmoidal dose-response relationship (FIG. 1B). To confirm the functional significance of the binding of LBW242 to IAPs, the effect of LBW242 binding on caspase activity in a cell-free system was assessed. In an assay in which the activity of caspase-9 was blocked by recombinant XIAP-BIR3, increasing doses of LBW242 resulted in caspase-9 activation with subsequent activation of caspase-3 and cleavage of a fluorogenic substrate (FIG. 1C).

Next, the effects of LBW242 in intact cells were assessed. LN827 glioma cells were exposed to LBW242 for 4 hours, and then endogenous caspase-9 was immunoprecipitated from whole cell extracts. Although LBW242 did not have any effect on the overall levels of caspase-9, or XIAP (FIG. 1, D and E), the abundance of endogenous XIAP bound to caspase-9 was reduced in cells treated with LBW242 (FIG. 1, D and F). These results establish the cellular permeability of LBW242 and the ability of LBW242 to disrupt endogenous binding of IAPs to caspase-9 in intact cells.

To determine the achievable tissue concentrations of LBW242 in the in vivo setting, we administered LBW242 parenterally to mice at a dose of 50 mg/kg/d. After 14 days of daily dosing, LBW242 achieved a long-term steady-state concentration that exceeded 60 μM in tumors (FIG. 1G). For treatment of intracranial tumors, the blood-brain barrier (BBB) is an impediment to drug bioavailability. It was determined that LBW242 was able to cross even the intact BBB and achieve tissue concentrations of approximately 25 μM in normal brain (FIG. 1G). The BBB is at least partially disrupted within brain tumors, suggesting that achievable brain tumor levels exceed 25 μM.

The effect of the representative IAP inhibitor LBW242 on glioma cell proliferation was assessed, and no effect on the growth of U87 cells (FIG. 1H) or LN827 cells (data not shown) was observed with LBW242 as a single agent at concentrations of up to 50 μM. Since in vivo steady-state tissue levels of LBW242 exceed 25-60 μM (FIG. 1G), since there were no stand-alone effects on glioma growth up to 50 μM, and since caspase activity was most efficiently reversed in vitro at 50 μM concentrations, we used an exemplary concentration of 50 μM for all subsequent experiments.

Although IAP inhibition had no stand-alone activity, it was hypothesized that apoptosis might be achieved by simultaneously increasing pro-apoptotic signals. Since PDGFR has a well-established role in gliomagenesis, and since withdrawal of growth factor signaling is pro-apoptotic in many systems (Klein et al., 2005) the combined effects of IAP and PDGFR inhibition on cell growth was assessed. As a single agent, imatinib inhibited cell growth at doses >10 The addition of LBW242, which had no effect on cell growth alone, resulted in a shift in the imatinib dose-response curve towards increased sensitization in LN827 and U87 cells (FIG. 2A). Over four days of treatment, only mild cytostasis was apparent in cells treated with either imatinib or LBW242 alone, compared to frank cell death observed in cells treated with both agents (FIG. 2B).

Next, the effect of the small molecule kinase inhibitor, imatinib, on the inhibition of PDGFR was examined. While treatment with imatinib had no effect on the overall abundance of PDGFR, the activation state of PDGFR was almost completely abolished by imatinib at 2.5 uM in LN827 cells (FIG. 2C). When administered as mono-therapy, inhibition of LN827 cell growth was observed at imatinib concentrations ≧20 μM (FIG. 2A). In contrast, the synergistic effects on cell growth when imatinib was combined with LBW242 was observed at imatinib concentrations of approximately 1.25-2.5 μM (FIG. 2A). The correlation of dosages causing PDGFR inhibition and synergistic inhibition of tumor growth suggests that the response seen occurs due to inhibition of PDGFR. LBW242 had no effect on PDGFR abundance or activity (FIG. 2C), suggesting that the synergistic effects of the combination are not due to LBW242 potentiating the inhibitory effects of imatinib on PDGFR activation.

To further confirm that the observed synergy resulted from PDGFR inhibition, the combination of IAP inhibitor LBW242 with an alternative PDGFR kinase inhibitor AMN107 (Weisberg et al., Cancer Cell. 2005 February; 7(2):129-41) was also tested (FIG. 2D). A synergistic inhibition of cell growth was again apparent with the combination treatment. Similar results were also seen when LBW242 was tested in combination with the PDGFR inhibitor dasatinib. Together, these results demonstrate that inhibition of IAPs in cancer cells, e.g., glioma cells, has little stand-alone activity, but inhibition of IAPs acts synergistically with inhibition of PDGFR, which is known to play a key role in gliomagenesis. Stand-alone activity was observed with imatinib alone, but only at concentrations >10 fold above that required for PDGFR inhibition, suggesting that “off-target” inhibition of other kinases contributes to this single agent activity.

Example 2 Imatinib Activates the Intrinsic Apoptosis Pathway in Cancer Cells, but Apoptosis Requires Concomitant Blockade of IAPs

Given the established role for PDGFR in gliomas, and in light of the above results, it was hypothesized that PDGFR inhibition may be producing a pro-apoptotic signal that was counteracted by downstream anti-apoptotic proteins. Multiple upstream pro-apoptotic signals converge at the level of the mitochondria, resulting in mitochondrial outer membrane permeabilization (MOMP) and release of the pro-apoptotic mediators cytochrome c and Smac/Diablo (FIG. 1A). It was therefore assessed whether imatinib induced MOMP by measuring cytoplasmic levels of cytochrome c and Smac/Diablo in cells following imatinib treatment. In LN827 cells, imatinib at 10 μM, which has no effect on cell growth (FIGS. 2A and B), led to a significant increase in both cytoplasmic cytochrome c and Smac/Diablo (FIG. 3A). Consistent with its mechanism of action, the IAP inhibitor LBW242 had no appreciable effect on cytochrome c or Smac/Diablo levels, either as a single agent or in combination with imatinib (FIG. 3A). The concentration of imatinib at which MOMP was observed was 2.5 μM (FIG. 3A), which was coincident with the concentration at which PDGFR activity was inhibited (FIG. 2C), and where synergistic killing with LBW242 was observed (FIG. 2A) in LN827 cells.

Although imatinib induced MOMP (FIG. 3A), there was no activation of caspase 3 or 7 when cells were treated with imatinib alone (FIG. 3B). In contrast, the addition of the IAP inhibitor LBW242 with imatinib resulted in significant activation of caspase 3/7 activity (FIG. 3B). To determine if the synergistic activation of caspase 3/7 activity resulted in apoptosis, the number of apoptotic cells staining positive with Annexin-V was measured. PDGFR inhibition with imatinib alone and IAP inhibition with LBW242 alone caused minimal change in basal apoptotic level, however, the combination of imatinib and LBW242 resulted in synergistic induction of apoptosis (FIG. 3C). A small increase in apoptosis was apparent with PDGFR inhibitor AMN107 alone, but again the addition of IAP inhibitor LBW242 resulted in the majority of tumor cells undergoing apoptosis (FIG. 3C).

Together, these results establish that imatinib activates the apoptosis cascade and MOMP, but that caspase 3 and 7 are not activated unless the activity of IAPB is simultaneously blocked. The combination of PDGFR and IAP inhibition produces synergistic induction of apoptosis.

Example 3 Receptor-Tyrosine Kinase (RTK) and IAP Inhibition Activates Caspases and Suppresses Tumor Growth Independent of Akt

Several RTKs have been implicated in gliomagenesis, therefore it was hypothesized that the synergistic effects of PDGFR and IAP inhibition could be generalized to other growth factor receptors. First we assessed the combination of IAP inhibition and blockade of the growth factor receptor IGF-1R with NVP-AEW541, a highly specific IGF-1R kinase inhibitor (Garcia-Echeverria et al., 2004). The combination of AEW541 and LBW242 led to caspase 3/7 activation and synergistically inhibited tumor cell growth (FIG. 4A). Next we tested blockade of the growth factor receptor EGFR with the dual EGFR and HER2 kinase inhibitor PKI166 (Bruns et al., 2000). PKI166 as a single agent had a pro-apoptotic effect, resulting in increased levels of caspase 3/7 activation. The addition of IAP inhibition, however, led to enhanced caspase 3/7 activation and a correlative enhanced inhibition of glioma cell proliferation (FIG. 4B). This effect is likely more pronounced in primary tumors in vivo, as it is known that glioma cells reduce EGFR overexpression in culture (Ishii et at., 1999).

Because PDGFR, EGFR and IGF-1R all activate Akt, and since Akt provides key anti-apoptotic signals, we asked whether the demonstrated induction of apoptosis and inhibition of cell growth occur secondarily to Akt inactivation. As shown in FIG. 4C, Akt is tonically phosphorylated in LN827 cells. Administration of imatinib with or without the IAP inhibitor LBW242 did not inhibit Akt phosphorylation, nor did it inhibit the downstream phosphorylation of Bad (FIG. 4C). Furthermore, the combination of LBW242 and the specific Akt inhibitor triciribine, did not demonstrate any notable synergistic effect on either caspase 3/7 activation or tumor cell proliferation (FIG. 4D). Thus the synergy between growth factor inhibition and IAP inhibition occurs independently of a change in Akt status.

Alternative mechanisms by which growth factor inhibition may lead to activation of the apoptotic pathway and mitochondrial permeabilization in tumor cells, e.g., gliomas, were also tested. Because Erk 1/2 is another downstream target of growth factor receptors, Erk 1/2 phosphorylation status was measured, and it was determined that treatment with imatinib did not inhibit phosphorylation of Erk 1/2 (FIG. 4E). It was next investigated whether treatment with imatinib led to a change in expression of a number of anti- or pro-apoptotic members of the BCL-2 family of proteins. A significant change in expression was not observed for any of the proteins tested (FIG. 4F).

Example 4 Growth Factor Receptor Inhibition with Imatinib Downregulates Expression of NOL3, a Protein that is Overexpressed in Cancer Cells

To comprehensively assess the effect of growth factor inhibition on a broad number of pro- and anti-apoptotic mediators, mRNA expression was assessed using a 96-well quantitative RT-PCR microarray (Alikhani et al., 2005). Treatment with imatinib 10 μM resulted in a significant change in the expression of only one gene tested: NOL3 (Table 1). Imatinib was found to downregulate NOL3 in 7 individual multi-well screens. NOL3 encodes Nucleolar Protein 3 (Apoptosis Repressor with CARD domain (ARC)), which is known to be highly expressed in normal cardiac, skeletal and neurological tissue (Hong et at., 2003; Koseki et at., 1998). An independent quantitative RT-PCR analysis confirmed that imatinib significantly reduced NOL3 mRNA expression (FIG. 5A). Western blot confirmed that the reduction in NOL3 transcription over time leads to a correlative decrease in NOL3 protein levels, but not of other anti-apoptotic proteins (FIG. 5B).

To validate the clinical relevance of NOL3 in cancer, the expression of NOL3 was evaluated in malignant glioma using mRNA expression data (Phillips et al., 2006; Sun et al, 2006). This analysis found that NOL3 was significantly overexpressed in malignant gliomas when compared with normal brain tissue (FIG. 5C). Evaluation of NOL3 expression in subsets of malignant glioma specimens revealed increasing expression with worsening grade of tumor (FIG. 5D). Similarly, high expression of NOL3 in tumor specimens correlated with inferior patient survival (FIG. 5E).

Table 1 depicts data obtained from mRNA microanalysis for expression of genes in the apoptotic pathway. Data represents the average gene expression levels for 3 separate samples treated with or without 10 μM imatinib for 36 hours.

TABLE 1 RNA Microarray Analysis AVG C

 without Fold Fold Up- or normalization 2{circumflex over ( )}-ΔC

Difference Down-Regulation Test Control Test Control Test Sample/ T-TEST Test Sample/ Symbol Well Sample Sample Sample Sample Control Sample p value Control Sample ABL1 A01 28.19 25.31 5.2E−03 1.1E−02 0.48 0.0796 −2.09 AKT1 A02 25.93 23.21 2.5E−02 4.7E−02 0.53 0.0812 −1.89 APAF1 A03 29.60 27.96 1.9E−03 1.7E−03 1.12 0.1378 1.12 BAD A04 32.50 29.81 2.6E−04 4.8E−04 0.54 0.1288 −1.84 BAG1 A05 28.24 26.39 5.0E−03 5.1E−03 0.97 0.1801 −1.03 BAG3 A06 28.52 26.84 4.1E−03 3.8E−03 1.09 0.1965 1.09 BAG4 A07 28.26 27.23 4.9E−03 2.9E−03 1.71 0.1687 1.71 BAK1 A08 31.60 29.32 4.8E−04 6.7E−04 0.72 0.1411 −1.39 BAX A09 25.10 23.80 4.4E−02 3.1E−02 1.43 0.2034 1.43 BCL10 A10 26.83 25.69 1.3E−02 8.3E−03 1.59 0.2257 1.59 BCL2 A11 31.28 30.53 6.1E−04 2.9E−04 2.08 0.4084 2.08 BCL2A1 A12 35.00 35.00 4.6E−05 1.3E−05 N/A N/A 3.50 BCL2L1 B01 26.30 25.41 1.9E−02 1.0E−02 1.89 0.4089 1.89 BCL2L10 B02 35.00 35.00 4.6E−05 1.3E−05 N/A N/A 3.50 BCL2L11 B03 33.80 32.89 1.1E−04 5.7E−05 1.86 0.1340 1.86 BCL2L2 B04 29.65 27.32 1.9E−03 2.7E−03 0.70 0.1334 −1.44 BCLAF1 B05 26.55 25.09 1.6E−02 1.3E−02 1.27 0.1262 1.27 BFAR B06 26.30 24.61 1.9E−02 1.8E−02 1.09 0.1478 1.09 BID B07 25.78 23.34 2.7E−02 4.3E−02 0.65 0.0784 −1.55 BK B08 35.00 35.00 4.6E−05 1.3E−05 N/A N/A 3.50 BIRC1 B09 35.00 35.00 4.6E−05 1.3E−05 N/A N/A 3.50 BIRC2 B10 33.60 31.51 1.2E−04 1.5E−04 0.82 0.0520 −1.22 BIRC3 B11 33.63 31.83 1.2E−04 1.2E−04 1.01 0.1117 1.01 BIRC4 B12 26.54 25.52 1.6E−02 9.4E−03 1.72 0.2803 1.72 BIRC6 C01 26.95 25.33 1.2E−02 1.1E−02 1.14 0.1393 1.14 BIRC8 C02 35.00 35.00 4.6E−05 1.3E−05 N/A N/A 3.50 BNIP1 C03 30.08 27.77 1.4E−03 2.0E−03 0.71 0.0992 −1.42 BNIP2 C04 25.58 24.18 3.1E−02 2.4E−02 1.32 0.1720 1.32 BNIP3 C05 23.58 21.46 1.3E−01 1.6E−01 0.81 0.0667 −1.24 BNIP3L C06 23.67 21.96 1.2E−01 1.1E−01 1.07 0.0379 1.07 BRAF C07 30.89 29.90 7.9E−04 4.5E−04 1.77 0.2579 1.77 CARD4 C08 33.59 31.80 1.2E−04 1.2E−04 1.01 0.1548 1.01 CARD6 C09 29.58 28.29 2.0E−03 1.4E−03 1.44 0.2363 1.44 CARD8 C10 29.39 28.13 2.2E−03 1.5E−03 1.46 0.1865 1.46 CASP1 C11 29.17 27.56 2.6E−03 2.3E−03 1.15 0.1185 1.15 CASP10 C12 31.12 29.84 6.8E−04 4.7E−04 1.44 0.1684 1.44 CASP14 D01 35.00 35.00 4.6E−05 1.3E−05 N/A N/A 3.50 CASP2 D02 27.33 24.98 9.4E−03 1.4E−02 0.69 0.0730 −1.45 CASP3 D03 27.37 24.92 9.1E−03 1.4E−02 0.64 0.0881 −1.55 CASP4 D04 25.49 25.25 3.4E−02 1.1E−02 2.97 0.7013 2.97 CASP5 D05 35.00 35.00 4.6E−05 1.3E−05 N/A N/A 3.50 CASP6 D06 28.55 26.88 4.0E−03 3.7E−03 1.10 0.1367 1.10 CASP7 D07 28.54 26.02 4.0E−03 6.6E−03 0.61 0.1135 −1.64 CASP8 D08 30.98 29.58 7.4E−04 5.6E−04 1.32 0.1070 1.32 CASP9 D09 30.71 28.86 9.0E−04 9.3E−04 0.97 0.1561 −1.03 CD40 D10 28.85 27.18 3.3E−03 3.0E−03 1.11 0.1995 1.11 CD40LG D11 35.00 35.00 4.6E−05 1.3E−05 N/A N/A 3.50 CFLAR D12 26.61 28.20 1.5E−02 1.5E−03 10.54  0.6743 10.54 CIDEA E01 33.18 32.74 1.6E−04 6.3E−05 2.58 0.6905 2.58 CIDEB E02 35.00 35.00 4.6E−05 1.3E−05 N/A N/A 3.50 CRADD E03 30.15 28.26 1.3E−03 1.4E−03 0.94 0.1088 −1.06 DAPK1 E04 32.47 30.71 2.7E−04 2.6E−04 1.03 0.1567 1.03 DFFA E05 25.52 24.17 3.3E−02 2.4E−02 1.37 0.1909 1.37 FADD E06 25.55 23.63 3.2E−02 3.5E−02 0.93 0.1479 −1.08 FAS E07 26.37 25.35 1.8E−02 1.1E−02 1.72 0.2207 1.72 FASLG E08 35.00 35.00 4.6E−05 1.3E−05 N/A N/A 3.50 GADD45A E09 25.76 24.43 2.8E−02 2.0E−02 1.39 0.2036 1.39 HKK E10 35.00 35.00 4.6E−05 1.3E−05 N/A N/A 3.50 IGFIR E11 27.41 26.77 8.9E−03 3.9E−03 2.24 0.4110 2.24 LTA E12 35.00 35.00 4.6E−05 1.3E−05 N/A N/A 3.50 LTBR F01 26.40 25.44 1.8E−02 9.9E−03 1.81 0.1970 1.81 MCL1 F02 26.33 24.55 1.9E−02 1.8E−02 1.02 0.2555 1.02 NOL3 F03 30.71 26.52 9.0E−04 4.7E−03 0.19 0.0589 −5.21 PYCARD F04 33.99 31.55 9.3E−05 1.4E−04 0.65 0.0011 −1.55 RIPK2 F05 29.98 27.94 1.5E−03 1.8E−03 0.85 0.1470 −1.17 TNF F06 33.81 32.77 1.0E−04 6.2E−05 1.70 0.1793 1.70 TNFRSF10A F07 33.61 32.19 1.2E−04 9.2E−05 1.31 0.1995 1.31 TNFRSF10B F08 25.87 24.51 2.6E−02 1.9E−02 1.36 0.2139 1.36 TNFRSF11B F09 31.81 29.48 4.2E−04 6.0E−04 0.70 0.0690 −1.44 TNFRSF1A F10 31.11 29.63 6.8E−04 5.4E−04 1.26 0.3894 1.26 TNFRSF21 F11 28.12 26.49 5.4E−03 4.8E−03 1.13 0.1069 1.13 TNFRSF25 F12 31.87 29.16 4.0E−04 7.5E−04 0.53 0.0928 −1.87 TNFRSF7 G01 34.76 33.97 5.4E−05 2.7E−05 2.03 0.0490 2.03 TNFRSF9 G02 30.89 27.62 7.9E−04 2.2E−03 0.36 0.0077 −2.77 TNFRSF10 G03 34.68 32.97 5.8E−05 5.3E−05 1.08 0.0104 1.08 TNFSF7 G04 27.02 24.87 1.2E−02 1.5E−02 0.79 0.0955 −1.26 TNFSF8 G05 35.00 35.00 4.6E−05 1.3E−05 N/A N/A 3.50 TP53 G06 26.32 24.49 1.9E−02 1.9E−02 0.99 0.0696 −1.01 TP53BP2 G07 30.38 29.19 1.1E−03 7.4E−04 1.53 0.3833 1.53 TP73 G08 34.67 33.80 5.8E−05 3.0E−05 1.92 0.0513 1.92 TRADD G09 26.11 24.66 2.2E−02 1.7E−02 1.28 0.1791 1.28 TRAF2 G10 28.27 26.74 4.9E−03 4.0E−03 1.22 0.2224 1.22 TRAF3 G11 26.17 24.81 2.1E−02 1.5E−02 1.36 0.1938 1.36 TRAF4 G12 27.10 25.86 1.1E−02 7.4E−03 1.49 0.1860 1.49 18SrRNA H01 11.70 9.82 4.7E+02 5.0E+02 0.95 0.2526 −1.05 HPRT1 H02 28.09 25.31 5.5E−03 1.1E−02 0.51 0.0615 −1.95 RPL13A H03 26.46 24.63 1.7E−02 1.7E−02 0.98 0.1298 −1.02 GAPDII H04 18.29 17.07 4.9E+00 3.3E+00 1.50 0.1850 1.50 ACTB H05 18.41 17.08 4.5E+00 3.2E+00 1.39 0.1238 1.39 ACTB H06 20.79 20.13 8.7E−01 3.9E−01 2.22 0.0214 2.22 ACTB H07 22.67 23.06 2.4E−01 5.1E−02 N/A 0.2580 4.60 ACTB H08 24.76 23.73 5.6E−02 3.2E−02 1.71 0.4045 1.71 ACTB H09 26.04 24.88 2.3E−02 1.5E−02 1.57 0.4852 1.57 ACTB H10 25.39 23.14 3.6E−02 4.9E−02 0.74 0.2515 −1.36 ACTB H11 32.54 31.98 2.5E−04 1.1E−04 2.38 0.7092 2.38 ACTB H12 35.00 35.00 4.6E−05 1.3E−05 N/A N/A 3.50

indicates data missing or illegible when filed

Example 5 NOL3 is an Important Mediator of the Synergy Between Growth Factor Receptor Inhibition and IAP Inhibition

It was then investigated whether the effect of imatinib on NOL3 expression is an important mediator of the observed synergy between growth factor receptor inhibition (e.g., mediated by imatinib) and IAP inhibition (e.g., mediated by LBW242). NOL3 was ectopically expressed in LN827 cells (FIG. 5F), and the effect on induction of apoptosis by imatinib and LBW242 was assessed. Transfection with NOL3 led to a marginal decrease in basal levels of apoptosis but had a far more significant impact on the proapoptotic effects of treatment with LBW242 and imatinib, with a 30% reduction in the number of cells undergoing apoptosis when compared with control cells (FIG. 5G).

To further test the importance of NOL3 expression to IAP inhibitor-imatinib synergy, we assessed whether decreasing NOL3 expression alone was sufficient to sensitize cells to LBW242. siRNA knockdown of NOL3 in LN827 cells led to decreased protein abundance (FIG. 5H). While NOL3 depletion alone did not significantly increase apoptosis (FIG. 5I), depletion of NOL3 combined with LBW242 resulted in a significant increase in cellular apoptosis (FIG. 5I). In contrast, NOL3 depletion had no effect on the induction of apoptosis by etoposide (FIG. 5J). Taken together, these results show that a reduction in NOL3 expression is necessary for the observed synergy between imatinib and the IAP inhibitor LBW242, and further that reduced NOL3 expression is sufficient to sensitize cells to the pro-apoptotic effects of IAP inhibitor treatment.

Example 6 Growth Factor Receptor Inhibition Synergizes with IAP Inhibition to Suppress Tumor Growth In Vivo

The combination of growth factor inhibition and IAP inhibition was tested in an orthotopic glioma model. LN827 cells were stereotactically implanted into the brains of mice. Tumor burden was serially followed using bioluminescence imaging. Animals with established tumors, characterized by logarithmically increasing tumor burden, were divided into treatment cohorts. One group was treated with AMN107 at 100 mg/kg per day by oral gavage; one group was treated with LBW242 at 50 mg/kg twice per day by oral gavage; one group was treated with vehicle; and one group was treated with the combination of LBW242 and AMN107. Consistent with the in vitro studies, monotherapy with either AMN107 or LBW242 alone had no appreciable effect on tumor growth (FIG. 6A and FIG. 6B). In contrast, animals treated with both AMN107 and LBW242 had complete cessation of tumor growth (FIG. 6A and FIG. 6B). These results establish that combined inhibition of growth factor receptors, e.g., PDGFR, and IAPs produces synergistic anti-tumor efficacy in vivo.

Example 7 Combination Treatment of Primary Human Glioma Neurospheres Supports Synergistic Activity of LBW242 and Imatinib

The treatment combination was assayed in primary human glioma tumor neurospheres. In neurospheres derived from 2 different patients with GBM, LBW242 and imatinib had stand-alone activity, and in combination they had additive effects in decreasing overall neurosphere numbers (FIG. 6C). To further confirm this finding, the combinatorial index of imatinib plus LBW242 was calculated in a total of 5 neurosphere cultures and 2 adherent cell lines. The effect was additive or synergistic in all but one of the cell cultures tested (Table 2).

TABLE 2 Combinatorial index for treatment with LBW242 plus imatinib in glioma cells Expected Observed survival survival Combinatorial Cells proportion proportion index Primary hBT69 0.065 0.07 1.07 (additive) Primary hBT74 0.306 0.147 0.48 (synergy) Primary hBT78 0.18 0.29 1.61 (antagonism) Primary hBT79 0.16 0.08 0.59 (synergy) Primary hBT85 0.29 0.121 0.41 (synergy) LN827 0.88 0.06 0.07 (synergy) U87 1.08 0.63 0.58 (synergy)

The combinatorial indices for LBW242 and imatinib were expressed as the ratio of observed/expected cells surviving, where the expected result was calculated as the proportion of surviving cells following treatment with LBW242 alone multiplied by the proportion of cells following treatment with imatinib alone.

The morphological appearance of some neurospheres treated with LBW242 in combination with imatinib suggested aggregates of dead cells (FIG. 6D). To specifically assess induction of apoptosis within these neurospheres, lysates from treated neurospheres were analyzed with an antibody specific for the activated form of caspase-3. Consistent with the data derived from glioma cell lines, there was no appreciable caspase-3 activation by imatinib or LBW242 alone, and minimal activation by AMN107 alone (FIG. 6E). However, marked activation of caspase-3 was apparent when either imatinib or AMN107 was combined with LBW242 (FIG. 6E). To determine whether the same synergistic effect on primary glioma neurospheres could be recapitulated in the in vivo setting, we orthotopically implanted stem cell-enriched neurosphere cultures of primary human glioma cells intracranially in nude mice. After establishing tumors for 12 days, animals were divided into cohorts that were treated with vehicle, AMN107, LBW242, or a combination of AMN107 and LBW242, as described above. All animals treated with either vehicle or single agents died within 60 days. However, 3 of 7 mice treated in the combination arm remained alive and well at 125 days follow-up, with no evidence of either disease or treatment toxicity (FIG. 6F). The survival benefit at 60 days or more was highly statistically significant (P=0.01, 2-tailed Fisher's exact test). Taken together, these results support the synergistic activity of PDGFR and IAP inhibition in both in vitro and in vivo models derived from glioma cell lines and primary human glioblastoma samples.

Example 8 NOL3 Expression Level Combined with IAP Expression Level in Patient Samples Predicts Clinical Outcome

Based on the finding that modulation of NOL3 expression and IAP activity induces a potent anti-tumor effect, it was next investigated whether the combination of IAP expression and NOL3 expression levels has an important impact on clinical outcomes. The effect on patient survival of NOL3 expression in combination with expression levels of the IAP survivin was assessed in an mRNA expression dataset (Phiilips et al, 2006) (FIG. 7). This analysis indicated that high-grade glioma patients whose tumors had low levels of both NOL3 and survivin had significantly longer survival than those with either high levels of NOL3 alone, high levels of survivin alone, or high levels of both. The estimated 3 year survival was 63% (95% CI 41-85%) for patients with low levels of NOL3 and survivin, versus 24% (95% CI 13-35%) for all others, with a median survival of 322 versus 72 weeks. As higher expression of NOL3 occurs in tumors of higher grade it was possible that the tumor grade accounted for the difference in survival. To examine this possibility, the same comparison was performed following stratification of patients by histological grade. Neither NOL3 (FIG. 8A) nor survivin (FIG. 8B) levels resulted in a significant difference in survival when assessed individually in stratified patient groups. However, the combination of both low NOL3 and low survivin levels led to significantly improved survival for both patients with either grade III tumors (median survival 460 versus 108 weeks, p=0.035) or for patients with grade IV tumors (median survival 115 versus 66 weeks, p=0.028) (FIG. 9). Thus the combination of NOL3 and survivin expression appears to confer a prognostic effect more significant than that resulting from histological grade alone.

Example 9 Synthesis of the IAP Inhibitors of the Invention

Described below is a synthesis procedure for LBW 242 (N-[1-cyclohexyl-2-oxo-2-(6-phenethyl-octahydro-pyrrolo[2,3-c]pyridin-1-yl)-ethyl]-2-methylamino-propionamide).

Analogous synthesis procedures can be used to prepare the other IAP inhibitors of the invention.

But-3-enyl-((S)-1-phenyl-ethyl)-amine (A)

To a solution of S-(−)-1-phenyl ethylamine (15.75 g, 130 mmol) in 150 mL of DMF at 0° C. is added K₂CO₃ (53.9 g, 390 mmol) in small portions. After stirring at 0° C. for 10 min, 4-bromobutene (13.5 g, 100 mmol) is added dropwise and followed by NaI (58.5 g, 390 mmol) in small portions. The reaction mixture, a white suspension, is heated to 95° C. and stirred overnight/16 hrs. The solution is cooled to RT and diluted with 200 mL of ether, and washed with 3×100 ml of water. The organic layer is dried over Na₂SO₄ and concentrated. The crude product is purified by distillation (65˜70° C. under high vacuum) to yield a colorless liquid (13.5 g, 76.7%).

[But-3-enyl-((S)-1-phenyl-ethyl)-amino]-acetic acid ethyl ester (B)

To a solution of But-3-enyl-((S)-1-phenyl-ethyl)-amine (6.37 g, 36.4 mmol) in 150 mL of DMF at 0° C. is added K₂CO₃ (10.0 g, 72.8 mmol) in small portions. After stirring at 0° C. for 10 min. ethylbromoacetate (8.35 g, 54.6 mmol) is added slowly. The reaction mixture, a white suspension, is stirred at r.t. overnight/16 hrs. The solution is diluted with 200 mL of ether, and washed with 3×100 ml of water. The crude product is purified by chromatography (hexane/CH2Cl2: 50/50) to give a pale liquid (8.5 g, 94.5%).

(2S,3R)-3-But-3-enyl-1-((S)-1-phenyl-ethyl)-pyrrolidine-2-carboxylic acid ethyl ester (C)

To a solution of diisopropylamine (3.6 g, 35.7 mmol) in THF (80 mL) at −40° C. is added BuLi (14.28 mL, 35.7 mmol, 2.5 M in hexane) slowly. The solution is warmed to 0° C. and stirred for 30 min to form an LDA solution. The LDA solution is cooled to −70° C. and added to a solution of [But-3-enyl-((S)-1-phenyl-ethyl)-amino]-acetic acid ethyl ester (7.8 g, 29.8 mmol) in THF (80 mL) slowly at −70° C. The light yellowish reaction solution is stirred at −20° C. for 30 min to become a deep yellow solution, and then cooled to −70° C. To the solution is added ZnBr₂ (16.76 g, 74.5 mmol) in ether (50 mL) dropwise at −70° C. After stirring at RT for 1.5 hrs, the reaction solution is cooled to 0° C. and added a solution of CuCN (3.47 g, 38.74 mmol) and LiCl (3.29 g, 77.48 mmol) in THF (80 ml) slowly. After stirring at 0° C. for 10 min, allyl bromide (7.26 g, 60 mmol) is added dropwise to the reaction solution, and warmed very slowly to r.t. After stirring overnight at r.t., the reaction is quenched by addition of 60 mL of saturated NH₄Cl and extracted with 3×150 mL of ether. The combined organic layers are concentrated. The crude product is purified by chromatography (hexane/EtOAc: 85/15) to give a colorless liquid (7.4 g, 82.6%). (ZnBr₂ is dried at 150° C. under high vacuum for 1 hour before use.)

(2S,3R)-1-((2E,4Z)-(S)-1)2-DimethyI-hexa-2,4-dienyl)-3-(3-oxo-propyl)pyrrolidine-2-carboxylic acid ethyl ester (D)

(2S,3R)-3-But-3-enyl-1-((S)-1-phenyl-ethyl)-pyrrolidine-2-carboxylic acid ethyl ester (1.0 g, 3.32 mmol) is dissolved in EtOH (10 mL) with HCl (0.5 mL, 37%), and cooled to −70° C. Ozone gas is bubbled though the solution for about 10 min or until the solution is turned very light blue color. The nitrogen gas is bubbled though the solution for 15 min to remove excess ozone in the solution. To the cool solution is added Zn dust (0.43 g. 6.6 mmol) and HCl (0.5 mL, 37%), and stirred at r.t. for 20 min. After filtration the solution is diluted with 50 mL of CH2Cl2 and washed with saturated NaHCO₃ (10 mL) and 2×20 ml of water. After dried and concentrated, a colorless liquid (1.0 g) is obtained without further purification for next step reaction.

(2S,3R)-3-(3-Phenethylamino-propyl)-1-((S)-1-phenyl-ethyl)-pyrrolidine-2-carboxylic acid ethyl ester (E)

To a solution of (2S,3R)-1-((2E,4Z)-(S)-1,2-Dimethyl-hexa-2,4-dienyl)-3-(3-oxo-propyl) pyrrolidine-2-carboxylic acid ethyl ester (1.g, crude) in EtOH (IO mL) is added phenethylamine (0.44 g, 3.65 mmol) at r.t. After stirring at r.t. for 30 min, NaBH₃CN (0.3 g, 4.87 mmol) is added in one portion. After stirring at r.t. for 1.5 Hrs, the reaction solution is diluted with 50 mL of ether and washed with 20 mL of brine. The ether layer is concentrated and the crude product is purified by chromatography (CH₂Cl₂/MeOH: 97/3) to give a pale liquid (405 mg, 30.0%).

(3aS57aS)-6-Phenethyl-1-((S)-1-phenyl-ethyl)-octahydro-pyrrolo[2,3-c]pyridin-7-one (F)

(2S,3R)-3-(3-Phenethylamino-propyl)-1-((S)-1-phenyl-ethyl)-pyrrolidine-2-carboxylic acid ethyl ester (340 mg, 0.83 mmol) is dissolved in 20 mL of MeOH/KOH/H₂O (10 mL/5 g/5 mL). After stirring at 80° C. for 2 hrs, the solution is cooled to 0° C. and neutralized by addition of HCl (37%) to pH=5. After concentration the crude product is dissolved in 1 mL of CH₂Cl₂, and filtered through a short silica gel plug and eluted with CH2Cl2/MeOH(93/7) to give a pale glassy solid (250 mg, 78.9%) as the acid.

To a solution (0.05-0.1 M) of acid (1 equivalent) in DMF at r.t. is added diisopropylethylamine (5 equivalents). After stirring at r.t. for 20 min, a solution (0.05˜0.1 M) of HOBT (1.2 equivalents) and HBTU (1.2 equivalents) in DMF is added to the reaction mixture, and continued to be stirred for 1.5 h (or monitored by TLC). The reaction solution is diluted with ether (1×5˜10 times by volume of the solution), and washed with water (twice ×3 by volume of the solution). The combined organic solution is concentrated. The crude product is diluted with CH2Cl2 and dried over Na2SO4, and purified by chromatography (CH2Cl2/MeOH:97/3) to give pure product (70-95% yield).

Procedure for Compound F Using 2-Hydroxyl Pyridine

A solution of (2S,3R)-3-(2-Phenethylamino-ethyl)-1-((S)-1-phenyl-ethyl)-pyrrolidine-2 carboxylic acid methyl ester (400 mg, 1.05 mmol) and 2-hydroxyl pyridine (100 mg, 1.05 mmol) in THF (I O mL) is stirred at 40° C. for 24 hrs. The reaction is diluted with 50 mL of ether and washed with 2×120 mL of water. After dried and concentrated to give a pale liquid (350 mg) without further purification for next step reaction.

(3aR,8aS)-7-Phenethyl-1-((S)-1-phenyl-ethyl)-decahydro-pyrrolo[2,3-c]a zepine (G)

To a solution (0.02M) of lactam (1 equivalent) in THF at −20° C. is added a solution (0.02M) of LiAlH₄ (2 equivalent) in THF slowly. After stirring at r.t. for 1.5 hrs, the solution is diluted with ether (1×5 times by volume of the solution) and washed with water (twice 2 times by volume of the solution), dried and concentrated. The crude product is purified by chromatography (CH₂Cl₂/MeOH:97/3) to give product (yield 70-90%).

(3aR,8aS)-7-Phenethyl-decahydro-pyrrolo[2,3-c]azepine (H)

A solution/suspension of reactant (<1 g) and Pd 10% on carbon (20% by weight) in MeOH (10 mL, with 2 drops of acetic acid) in a 1000 ml round flask is vigorously stirred at r.t. under hydrogen gas (at atmosphere pressure) from a balloon for 4-8 hrs. After degassed by house vacuum for 10 min, the reaction mixture is filtered to remove catalyst and concentrated. The crude product is diluted with CH₂Cl₂/H₂O (8/2, reasonable amount) and neutralized with 10% NH4OH to pH=7-8. After dried and concentrated to give product (80% -quantitative yield) without purification for the next step reaction.

LBW 242

Prepared from compound H using the scheme described below:

Compound (7)

To a solution of 6 in dichloromethane (25 mL) is added sequentially diisopropylethylamine (4.17 mL, 24 mmol), t-Boc-L-cyclohexylglycine (1.54 g, 6 mmol), and a solution of 0.45 M HOBt/HBTU in DMF (16 mL, 7.19 mmol). The mixture is stirred overnight at room temperature, then diluted with EtOAc (200 mL) and washed sequentially with 1 M aq. citric acid (50 mL), water (50 mL), aq. Sat. NaHCO₃ (50 mL) and brine (2×50 mL). The organic layer is dried and concentrated under vacuum. The residue is purified by flash chromatography (silica gel; Hexane/EtOAc 1:9) to provide a yellow oil. The yellow oil is dissolved in dichloromethane (20 mL), TFA (10 mL) is added and the mixture is stirred at room temperature for 3 h. The mixture is concentrated and the residue is dissolved in dichloromethane (100 mL) and neutralized with saturated sodium bicarbonate. The solution is extracted with dichloromethane (3×50 mL). The organic extracts are combined, dried and concentrated under vacuum to provide 1.75 g (79% two steps) of the title compound which is used in next step without further purification or characterization.

LBW 242

To a solution of 7 (1.75 g, 4.74 mmol) in dichloromethane (25 mL) is added sequentially diisopropylethylamine (3.30 mL, 19 mmol), t-Boc-N-methyl-L-alanine (0.97 g, 4.74 mmol), and a solution of 0.45 M HOBt/HBTU in DMF (13 mL, 5.691 mmol). The mixture is stirred overnight at room temperature. The mixture is diluted with EtOAc (200 mL) and washed sequentially with 1 M citric acid (50 mL), water (50 mL), aq. Sat. NaHCO3 (50 mL) and brine (2×50 mL). The organic layer is dried and concentrated under vacuum. The residue is dissolved in dichloromethane (20 mL), TFA (10 ml) is added and the mixture is stirred at room temperature for 3 hours. The mixture is concentrated and the residue is dissolved in dichloromethane (100 mL) and neutralized with saturated sodium bicarbonate. The solution is extracted with dichloromethane (3×50 mL). The organic extracts are combined, dried and concentrated under vacuum. The residue is purified by HPLC (C-18 silica gel, 20% CH3CN/H2O in 0.5% TFA) to provide 1 g (36% two steps) of the title compound as TFA salt.

EQUIVALENTS

The invention has been described herein with reference to certain examples and embodiments only. No effort has been made to exhaustively describe all possible examples and embodiments of the invention. Indeed, those of skill in the art will appreciate that various additions, deletions, modifications and other changes may be made to the above-described examples and embodiments, without departing from the intended spirit and scope of the invention as recited in the following claims. It is intended that all such additions, deletions, modifications and other changes be included within the scope of the following claims. 

1. A method of predicting responsiveness to an IAP inhibitor in a subject having cancer and treating said subject having cancer, the method comprising (a) measuring the level of NOL3 expression in a cancer cell-containing sample from said subject; (b) comparing the level of NOL3 expression in said cancer-cell containing sample to a reference level of NOL3 expression in a sample from a subject without the cancer, wherein an equivalent or lower level of NOL3 expression measured in the cancer cell-containing sample relative to said reference level predicts responsiveness of the subject to the IAP inhibitor; and (c) administering a therapeutically effect amount of the IAP inhibitor to said subject having cancer when the level of NOL3 expression measured in the cancer cell-containing sample is lower than the reference level of NOL3 expression; wherein the IAP inhibitor is a compound of formula (II)

or pharmaceutically acceptable salts thereof, wherein R₁ is H or C₁ C₄ alkyl; R₂ is H or C₁ C₄-alkyl; R₃ is H or C₁ C₄ alkyl; A is 5- or 6-membered heteroaryl containing 1-4 ring heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur, the heteroaryl being unsubstituted or substituted with lower alkyl, amino, or halo; D is O, C(O), or NCH₃; A₁ is phenyl or 5- or 6-membered heteroaryl containing 1-4 ring heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur, the phenyl and the heteroaryl being unsubstituted or substituted with halogen; M is H; and n is
 0. 2. A method of selecting a subject having cancer for a treatment regimen and treating said subject having cancer, comprising (a) measuring the level of NOL3 expression in a cancer cell-containing sample from said subject; (b) comparing the level of NOL3 expression in said cancer cell-containing sample to a reference level of NOL3 expression in a sample from a subject without the cancer; (c) selecting said subject having cancer for a treatment regimen when the level of NOL3 expression in the cancer cell-containing sample is equivalent or lower than the reference level of NOL3 expression; and (d) administering a therapeutically effective amount of the IAP inhibitor to said subject having cancer selected in step (c); wherein the IAP inhibitor is a compound of formula (II)

or pharmaceutically acceptable salts thereof, wherein R₁ is H or C₁ C₄ alkyl; R₂ is H or C₁ C₄-alkyl; R₃ is H or C₁ C₄ alkyl; A is 5- or 6-membered heteroaryl containing 1-4 ring heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur, the heteroaryl being unsubstituted or substituted with lower alkyl, amino, or halo; D is O, C(O), or NCH₃; A₁ is phenyl or 5- or 6-membered heteroaryl containing 1-4 ring heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur, the phenyl and the heteroaryl being unsubstituted or substituted with halogen; M is H; and n is
 0. 3. (canceled)
 4. The method of claim 1, wherein the cancer is a carcinoma.
 5. The method of claim 1, wherein the cancer is a glioma.
 6. The method of claim 1, wherein the cancer is a hematologic malignancy.
 7. The method of claim 2, wherein the cancer is a carcinoma.
 8. The method of claim 2, wherein the cancer is a glioma.
 9. The method of claim 2, wherein the cancer is a hematologic malignancy.
 10. The method of claim 1, wherein the IAP inhibitor is (S)—N—((S)-1-Cyclohexyl-2-{(S)-2-[4-(4-fluoro-benzoyl)-thiazol-2-yl]-pyrrolidin-1-yl}-2-oxo-ethyl)-2-methylamino-propionamide, or a pharmaceutically acceptable salt thereof.
 11. The method of claim 2, wherein the IAP inhibitor is (S)—N—((S)-1-Cyclohexyl-2-{(S)-2-[4-(4-fluoro-benzoyl)-thiazol-2-yl]-pyrrolidin-1-yl}-2-oxo-ethyl)-2-methylamino-propionamide, or a pharmaceutically acceptable salt thereof. 